Getting the Most from QuickBooks Payroll 2008
Filing and Paying Your Payroll Taxes in QuickBooks 2008
In QuickBooks 2008, we've made enhancements to the way you pay your payroll taxes and file your payroll tax forms.
These enhancements simplify payroll processing, so you can feel confident that your payroll taxes and forms are complete and accurate, and so you can submit them to the agency on time.
Depending on your payroll service plan, you can do the following in QuickBooks 2008:
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Set up scheduled payments for your payroll tax and non-tax liabilities. You can set up a scheduled payment for your federal 940 payment, for example (Figure 1). Each time you run a payroll or make a payroll liability adjustment in QuickBooks, any 940 tax liability payment amounts accrue and appear in the QuickBooks Payroll Center.

Figure 1: Scheduled Payment for a Federal 940 PaymentYou can, however, continue to create custom payroll liability checks for payroll tax and non-tax liabilities that you don't set up as scheduled payments in QuickBooks—for example, a one-time payroll tax or fee.
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Set up supported, scheduled tax payments to be paid electronically (e-pay). When you set up scheduled tax payments for e-pay, you can prepare, submit, and track the payment transaction from QuickBooks (Figure 2).

Figure 2: Electronically Pay Scheduled Tax Payments -
Set up supported federal and state payroll tax forms for electronic filing (e-file). When you set up payroll tax forms for e-file, you can prepare, submit, and track the submission from QuickBooks (Figure 3).

Figure 3: Electronically File Payroll Tax Forms
FAQs: New Payroll Tax Payment and Filing Features Available with QuickBooks 2008
To help you understand how to use the new payroll tax payment and filing features, we've answered the top questions that QuickBooks Payroll customers may have about these payroll tasks.
Q1: How do I pay my payroll taxes in QuickBooks?
Q2: What is a scheduled payment?
Q3: Do I have to set up my payroll liabilities as scheduled payments?
Q4: Which payroll taxes are supported in QuickBooks?
Q5: How do I set up a scheduled payment in QuickBooks?
Q6: Can I electronically pay (e-pay) my payroll taxes?
Q7: Can I e-pay my non-tax payroll liabilities, such as 401(k) contributions or my health care premiums?
Q9: What happens to the e-payment after it is submitted?
Q10: How do I pay a scheduled payment?
Q11: Can I electronically file (e-file) my payroll tax forms?
Q12: How do I set up my payroll tax forms for e-file?
Q13: How do I e-file a payroll tax form?
Q1: How do I pay my payroll taxes in QuickBooks?
A: QuickBooks automatically tracks the amounts of payroll taxes and other liabilities that accrue on each paycheck, such as federal and supported state payroll taxes, 401(k) contributions, and health insurance. When their due date arrives, you just need to pay them. Depending on your payroll service subscription, you have three ways to pay your payroll taxes and payroll liabilities in QuickBooks:
- Pay a scheduled payment that you've set up in QuickBooks.
- Pay supported payroll taxes electronically (e-pay).
- Pay an unscheduled (custom) payroll tax or other liability.
Note: You may already be familiar with the unscheduled (custom) payroll liability workflow. Prior to QuickBooks 2007 and 2008, this was the method that you used in QuickBooks to pay your payroll taxes and other liabilities.
Q2: What is a scheduled payment?
A: A scheduled payment is one payroll tax or non-tax liability—or several payroll taxes or non-tax liabilities that are paid together, at the same time, to the same agency. For example, you typically pay your federal withholding, Social Security, and Medicare taxes at the same time to the IRS.
QuickBooks enables you to set up scheduled tax payments, so the taxes are tracked and paid in the same payment to the agency. For example, when you set up your federal 941 (or 944) payment as a scheduled payment in QuickBooks and then run a payroll, any accrued federal withholding, Social Security, or Medicare taxes appear in the Pay Scheduled Liabilities section of the Payroll Center, as shown in Figure 4.

Figure 4: Pay Scheduled Liabilities
You must have an active payroll service subscription to set up scheduled payments in QuickBooks.
Q3: Do I have to set up my payroll liabilities as scheduled payments?
A: We recommend that you set up scheduled payments for your payroll taxes, but you don't need to set up your payroll liabilities as scheduled payments. You can also make a custom (unscheduled) tax payment if, for example, you have a one-time payroll tax or fee, or you need to make an adjustment to a payroll tax.
To electronically pay (e-pay) a supported payroll tax liability, you must first set up the tax as a scheduled payment.
Q4: Which payroll taxes are supported in QuickBooks?
A: QuickBooks supports federal and selected state payroll taxes and agencies. For the most current information about availability and requirements for your state payroll tax agencies, visit the Payroll Tax Support Web site.
For information about which taxes you can electronically pay (e-pay) from QuickBooks, visit the QuickList page of the Payroll Tax Support Web site.
Intuit continues to add support for more states and will notify you when agencies become available or when currently supported agencies change their requirements for electronic payments submitted from QuickBooks.
Q5: How do I set up a scheduled payment in QuickBooks?
A: You set up your scheduled payments by using the QuickBooks payroll setup interview, which guides you step-by-step through the process.
To set up scheduled payroll tax or non-tax liability payments in QuickBooks:
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Open the Payroll Center. (From the Employees menu, select Payroll Center, as shown in Figure 5.)

Figure 5: Opening the Payroll Center -
In the Pay Scheduled Liabilities section of the Payroll Center, click the Related Payment Activities drop-down arrow and then click Edit Payment Due Dates/Methods (Figure 6).
QuickBooks closes all embedded windows and then opens the payroll setup interview.

Figure 6: Selecting Edit Payment Due Dates/Methods to Open the Payroll Setup Interview - Follow the instructions provided in the payroll setup interview.
Q6: Can I electronically pay (e-pay) my payroll taxes?
A: You can electronically pay (e-pay) certain federal and state payroll taxes directly from QuickBooks. For information about which taxes are supported, visit the QuickList page of the Payroll Tax Support Web site.
To e-pay your payroll taxes from QuickBooks, you must have the following:
- QuickBooks 2007 (or later)
- An active payroll service subscription that supports e-pay
- For additional information about e-pay requirements, visit the Payroll Tax Support Web site.
Intuit continues to add support for more states and will notify you when agencies become available or when currently supported agencies change their requirements for e-payments submitted from QuickBooks.
Q7: Can I e-pay my non-tax payroll liabilities, such as 401(k) contributions or my health care premiums?
A: No. At this time, you can e-pay only selected federal and state payroll taxes.
Q8: How does e-pay work?
A: To e-pay your payroll taxes, you first need to set up the payroll tax as a scheduled payment. The payroll taxes will accrue, and then you create and submit an e-payment.
When you set up the payroll tax as a scheduled payment in QuickBooks:
- Make sure that you have the appropriate payroll service subscription.
- Make sure your QuickBooks company information is current in your company file. You can double-check your information: From the File menu, click Company Information. When you submit an e-payment to the agency, QuickBooks sends certain company information required by the agency, such as an e-mail address that the agency can use to contact you about the payment. Be sure that the information in your company file is current and complete.
- Set up your scheduled tax payments for e-pay in payroll setup.
- Enroll in the tax agency's electronic payment program (if the tax agency requires enrollment). Not all agencies require enrollment, but for those agencies that do require enrollment, it's important that you've completed the entire process before you submit an e-payment from QuickBooks. Enrollment instructions are included in payroll setup and on the Enrollment page of the Payroll Tax Support site.
After you set up scheduled tax payments in QuickBooks, the payments appear in the Payroll Center anytime you accrue the payroll taxes included in the scheduled tax payment. For example, payroll taxes can accrue when you pay your employees or make adjustments to a payroll liability.
Lastly, make an e-payment:
- Create and submit an e-payment. You can create scheduled payments for e-pay and printed liability checks at the same time.
- Check the e-payment status.
Q9: What happens to the e-payment after it is submitted?
A: Figure 7 shows where information flows after you submit an e-payment.

Figure 7: The Flow of Information After an E-Payment Is Submitted
The following steps occur:
- QuickBooks sends the payment information to Intuit.
- Intuit sends the payment information, in batch mode, to the agency.
- The agency processes the payment and, when accepted by the agency, the agency initiates the ACH debit transaction with the bank account set up for e-payments.
Important: Intuit does not access or hold your funds during the e-payment transaction. - The agency returns the e-payment status to Intuit.
When you check the e-payment status, QuickBooks retrieves the current status from Intuit and returns the status to the E-Payment History window.
Q10: How do I pay a scheduled payment?
A: To pay a scheduled payment, follow these steps:
- Open the Payroll Center. (From the Employees menu, select Payroll Center.)
- In the Pay Scheduled Liabilities section, select the scheduled payment you want to pay. A checkmark identifies those payments you're paying now (Figure 8).

Figure 8: Selecting a Scheduled Payment to Pay - Click View/Pay.
- In the Liability Payment window, review the payment (Figure 9).

Figure 9: Reviewing a Payment - Select the payment method—E-payment or Check, if the options are available.
- Click Save & Next to save the check and display the next payment, or click Save & Close if this is the last check.
or
Click E-pay to start the electronic submission.- In the E-pay Login window, enter your login information.
Important: It's very important to enter your login details carefully. If you enter your details incorrectly, your e-payment could be rejected by the agency. - Click Submit. Your e-payment is sent to Intuit for processing.
- Review the information in the E-pay Confirmation window.
- In the E-pay Login window, enter your login information.
- After you create your last check or e-payment, the Payment Summary window appears. Review your payments and click Close.
Q11: Can I electronically file (e-file) my payroll tax forms?
A: You can electronically file (e-file) certain federal and state payroll forms directly from QuickBooks. For information about which payroll tax forms are supported, visit the QuickList page of the Payroll Tax Support Web site.
To e-file your payroll tax forms from QuickBooks, you must have the following:
- QuickBooks 2007 (or later)
- An active payroll service subscription that supports e-file
- Internet access
For additional information about e-file requirements, visit the Payroll Tax Support Web site.
Intuit continues to add support for more states and will notify you when agencies become available or when currently supported agencies change their requirements for payroll tax forms electronically submitted from QuickBooks.
Q12: How do I set up my payroll tax forms for e-file?
A: You set up your payroll tax forms for e-file by using the QuickBooks payroll setup interview, which guides you step-by-step through the process. When you set up the form for e-file, you start the enrollment process, if the agency requires enrollment in its e-file program.
Visit the Enrollment page on the Payroll Tax Support site to see if your agency requires enrollment.
To set up your payroll tax forms for e-file:
- Open the Payroll Center. (From the Employees menu, select Payroll Center.)
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In the File Tax Forms section, click the Related Form Activities drop-down arrow and then click Edit Filing Methods (Figure 10).

Figure 10: Selecting Edit Filing Methods to Open the Payroll Setup InterviewQuickBooks closes all windows and then opens the payroll setup interview.
- Follow the instructions in the payroll setup interview.
Q13: How do I e-file a payroll tax form?
A: To e-file a payroll tax form, follow these steps:
- In the Payroll Center, click Process Payroll Forms and then select the type of form you want to prepare from the Select Form Type window.
- In the Select Payroll Form window, choose the form you want to file.
- In the Payroll Tax Form window, review the data.
- Click View details about this form in the Payroll Tax Form window for information about how QuickBooks calculates the numbers on the form and for instructions on what you need to do to complete the return.
- Click Submit Form.
- In the Submit Form or Print/E-file Form window, click E-file or E-file Federal Form.
- In the agency login window, enter the agency login information required by the agency.
Important: It's very important to enter your login details carefully. If you enter your details incorrectly, your form may be rejected by the agency or may not be processed in a timely manner. - Click Submit.
- Review the information in the E-file Confirmation window.
- Click Close to close the confirmation window.
- Click Print to print copies of your form for your records.
- Close the Payroll Tax Form window.
Q14: What happens when a payroll tax form is e-filed?
A: Figure 11 shows where information flows after you submit a payroll tax form electronically.

Figure 11: The Flow of Information After a Payroll Tax Form Is E-Filed
The following steps occur:
- QuickBooks sends the information to Intuit.
- Intuit sends the payroll tax form information, in batch mode, to the agency.
- The agency processes the form and then returns the status to Intuit.
- When you check the e-file status, QuickBooks retrieves the current status from Intuit and returns the status to the E-filing History window.
Q15: How do I check the status of my e-payment or e-filing?
A: After you submit your payroll tax payment or form, you can check the status from within QuickBooks.
To check the status from QuickBooks:
- Open the Payroll Center. (From the Employees menu, click Payroll Center.)
- In the Pay Scheduled Liabilities section, click Check E-payment Status.
or
In the File Tax Forms section, click Check E-filing Status.
QuickBooks retrieves the current status of the payment or filing and displays the information in the history window.
Processing times for electronically filed payroll tax forms vary from agency to agency. Some agencies process forms immediately, so you may be able to check the status right after you submit the form from QuickBooks. Other agencies can take as many as 48 hours after the form is submitted to process the e-payment, so you may want to wait 24 to 48 hours before you check the status.
We'd Like Your Feedback
QuickBooks Payroll 2008 includes a redesigned Pay Liabilities workflow to make it easier and more efficient for QuickBooks Payroll users to file payroll tax forms. We hope you are now more familiar with how to use these features and can take advantage of the benefits.
Did the information in this short lesson help you understand the new workflows? Please let us know.
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