A paycheque isn't reflected in the balance of your bank account
If you paid an employee but your payroll bank account balance is unchanged, you may have selected a bank or credit card account other than the one you intended.
To determine which account has been used for the paycheque, locate the payment in the Find Transactions window and click the arrow to the left of one of the payroll categories associated with the paycheque. The transaction will appear in the Pay Employees window as you originally entered it.
Once a paycheque is recorded, the bank 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 paycheque, then reenter it with the correct information. Whether you will need to delete the paycheque or reverse it depends upon how your preferences have been set. (Choosing changeable or unchangeable transactions)