I overpaid our 4Q2016 payroll taxes. The 941 was submitted with the correct amount and that the refund would be applied to the next payment. How do I do that?

Hi fellowshipinocal,

You can enter a prior payment for the overpaid amount or apply it as a credit to the payroll tax liability. 

To do enter a prior payment:

1. Click Help at the top menu bar, then select the last option which is About (your QuickBooks version).
2. Once the green screen with your QuickBooks information appears, press Ctrl + Alt + Y at the same time.
3. Click Next until you're under the Enter prior payments window.
4. Click Create Payment. If you have an amount in the table, click Next Payment until you see an empty table.
5. Change the Payment Date and For Period Ending date.
6. Choose your tax items under the Item Name column and enter the Amounts. You can enter a memo if you want (see attached screenshot).
7. Click Accounts Affected, and choose Affect liability accounts but not the bank account.
8. Click OK, then Done, and Finish.

To apply the amount as a credit to the payroll tax liability, please check this out: Resolve a payroll tax overpayment.

Please let me know if you have other questions.