When you are invoicing a job or list of jobs and the customer has a credit balance, you can choose to apply a credit or multiple credits to this invoice at the point of actually creating the invoice.
When the Invoice screen appears, go to Payment Details tab and click Apply Credits or press F6 on your keyboard.
The Select Credit/Prepayments screen will be displayed.
Select the credit you want to apply and tick, then click OK. This will apply this credit to this invoice, the Paid Today field in the Invoice screenwill show the total applied, and the balance due will reduce.