Hello there, @EBuilders.

It’s nice to have you in the Community. I’m here to assist you in removing the old payroll liabilities showing as overdue in your account.

Since you referenced that the payment was made and liabilities still show as overdue, you can enter historical tax payments to mark them as paid.

Here’s how:
1.    Click the Help menu at the top and select About QuickBooks.
2.    On your keyboard, press Ctrl + Alt + Y to open the Setup YTD Amounts window.
3.    Select Next until you reach the Enter prior payments section.
4.    Click Create Payment.
5.    Enter the Payment Date and For Period Ending date accordingly.
6.    In the Taxes and Liabilities field, choose the payroll tax item you’ve already paid and then enter the amount.
7.    Click on Accounts Affected button and select Do not affect accounts. By doing so, the prior payments will not affect your balances or show up in the bank register.
9.    Continue to the next by selecting Next Payment. Once all payments have been entered, click Done to save your work.
10.    Hit Finish to close the window.

For additional information, as well as screenshots for the steps above, please visit the following link: Enter historical tax payments in QuickBooks Desktop Payroll.

This information should be able to answer your questions on how to remove paid liabilities showing as overdue in the Pay Liabilities section.

Please let me know how it goes by leaving a comment below. If you need anything else, don’t hesitate to ask. I’ll be here to help. Have a most pleasant day!