To determine whether a liability was paid with Write Checks or Bill Payment:
- Select Vendors > Vendor Center.
- Choose the vendor's name.
- In the Type column, ensure all are listed as Liability Check.
- If there is a Check, double-click to view the transaction.
- Verify that this transaction was created to pay payroll liabilities.
If a liability was paid through the Write Checks screen or Bill Payments:
- Back up the Company file.
- Go to Write Checks or Bill Payment and use the Previous and Next keys to locate the payment. Note the amount paid and the expense account used.

- In the Payroll Center, go to the Pay Liabilities tab. And select the overdue liability that was paid through Write Checks.
- Select the View/Pay button, which brings up the liability check.
- Select the Expense tab.
- In the Account column, select the drop-down ▼ arrow. And choose the account used in Write checks. In the Amount field, enter a negative amount equal to the amount of the liability check.

(Note: If the liability shown as being owed was only partially paid through Write Checks, enter the actual amount paid through Write Checks as a negative instead of the whole amount shown as being owed.) - Select the Recalculate button to zero the check amount.
- Uncheck the To be printed box.
- If the check number field populates, remove the check number.
- Date the transaction to be the same date as the payment that was already entered into the QuickBooks Desktop bank register.
- Select Save > Close.
To eliminate this from happening the next time:
QuickBooks Desktop payroll works best when all payroll activity is performed from within the payroll menus. This includes paying accrued payroll taxes to the respective taxing authorities. If you write checks or use the Enter/Pay Bills functionality to pay for the liabilities and the QuickBooks-created Payroll Liabilities account was assigned, the following warning message appears:

The message warns but does not prevent you from using the wrong type of payment (i.e., Write Checks or Enter/Pay Bills) when attempting to make payroll liability payments. When you select the Pay Payroll Liabilities button in the warning message, you will be directed to the Select Date Range for Liabilities dialog. The message directs you to the Pay Payroll Liabilities feature to create a payroll liability check.