You can assign a portion or all of the total payment to a client's invoice, reflecting it as a credit balance in the client's profile.
Go to Account > Invoices and select the relevant invoice. (You can also access the client's invoice through their profile.)
Click the apply credit
If the credit covers the whole fee, the invoice will be marked as paid. If there is an additional amount due, allocate the balance by clicking on +Add payment
Click the Save button or Save & send