You can apply the deposit as you normally should using the standard procedure. Choose Tasks and click Receipts. Enter Customer ID, then enter the check number in the Reference Number field. Add the date in the Deposit Ticket ID field. Enter the payment method in the Payment Method field and the account to which the money will be deposited. Use the Cash Account field. Enter the amount, then select the invoice where is should be applied to. After the procedure completes, click Post and that's it.