Hey there, @Embrace.
You've come to the right place. I can share some information to get this payroll liability issue sorted out and get you back to business.
QuickBooks will calculate taxes based on the rate that you've set up for a payroll item. In situations like this, I'd suggest running a payroll detail review to review the total withholding taxes. This way you'll be able to determine the taxes for a certain employee that needs to be adjusted.
Once you've verified the difference from your employee's payroll, you can record a payroll liability adjustment to match the amount that was paid from the agency.
Moving forward, you'll have the option to leave the rate section of your payroll item and enter the amount manually upon creating the paychecks to match your payroll liability.
If you need additional assistance with this process, feel free reach out to our Customer Care Team. They have an extra tool like screen-sharing that can help you with the steps.
These resources should guide you with fixing your payroll liabilities.
Of course, I'm just a reply away if you have any other questions with this concern or any QuickBooks related thing. I want to ensure you're taken cared of. Have a good one.