You can change the employee's payment method to cash or cheque if you have already paid them outside of your bank submission. This will exclude them from your bank submission. Please follow the steps below:
Go to the Payroll module and click Pay Record.
Double-click the employee ID.
Click Bank Allocation, then click Delete
Click Yes and click New.
Select Cheque, or Cash, then click Save
Click Recalculate then click Yes and Confirm.