First time users / payroll users are often confused how to pay the liabilities. I recently responded to the following questions: "Can you tell me how to pay my payroll liabilities? I think I use "write checks" and then hit the appropriate accounts, but I am not sure."
The answer is no…. do not use write checks! In order to properly clear the liability, you need to pay payroll liabilities with a liability check instead of a regular check.
Employees > Payroll Taxes and Liabilities > Pay Scheduled Liabilities
As a side note, sales tax liabilities also need to be paid with a liability check
Vendors > Sales Tax > Pay Sales Tax.