An employee payment isn't reflected in the balance of your checking account
If you paid an employee but your payroll account balance is unchanged, you may have selected a checking or credit card account other than the one you intended.
To determine which account has been used for the employee payment, locate the payment in the Find Transactions window and click the arrow to the left of one of the payroll categories associated with the payment. The transaction will appear in the Pay Employee window.
Once a employee payment is recorded, the checking account assigned to it can't be changed. If you've made a mistake and you wish to correct it, you'll have to either delete or reverse the payment, then reenter it with the correct information. Whether you will need to delete the payment or reverse it depends upon how your preferences have been set. (Choosing changeable or unchangeable transactions)