When you pay payroll liabilities with a regular check, your reports are usually correct so you don’t want to affect accounts with the adjustment. You just want to remove the liabilities you paid incorrectly. Make sure to pay your payroll liabilities through Employees > Payroll Taxes & Liabilities > Pay Scheduled Liabilities in the future.

You really should enter each payroll individually, otherwise reconciling your bank account is going to be a nightmare. In this case, I recommend entering a check for each debit from your bank account. You’d enter the gross payroll as a positive number and employee withholding as a negative number. The net check would be what was actually debited from your account.

When you pay your payroll taxes ($59903.30) you’d enter two accounts – $50558.74 for payroll tax liabilities and $9344.60 for payroll tax expense.

But if you want to enter a journal entry for the entire year, it should look like this:

Debit – payroll expense ($168000)
Debit – payroll taxes ($9344.60)
Credit – bank account ($177344.60) – $117441.26 net pay + $59903.34 payroll taxes

I recommend switching to QuickBooks Assisted Payroll. It’s integrated with QuickBooks so you don’t need to enter journal entries. It’s also less expensive than Paychex.

Here are the standard fees. We can get you 20% off your monthly service fees for the first year: