Assuming you have a payroll subscription….
When you pay payroll taxes in QuickBooks there is a way to do this so it tracks better. Click employees and pay payroll taxes, choose unscheduled payroll taxes, and enter the date of the pay checks. (everything is based on the check date)
From there you can select the items you want to pay. ie. 941 tax – select federal withholding, social security (both sides), Medicare (both sides).
Then create a check using the date that you made the payment. Usually it is an EFT (drafted out of bank account), save.
Continue through each area. To check to see if you are through, click reports, payroll and select payroll liability balances. The only things left on there should be your quarterly accruals (SUTA) and other withholdings that aren’t paid through there like health insurance.