1. Open the Receipts window.
2. Select the customer.
3. Click the Receipt menu at the top.
4. Select Enter Deposits. 
5. Enter the amount in Deposit Amount at the bottom.
6. Enter the Deposit Reference No..
7. Click Post or Process.
8. If there's an invoice to be paid and you need only to deposit the remaining amount:
   • Click the invoice to be paid off to fill up the amount received
   • Enter the difference (overpaid) amount in the deposit field and the deposit reference number
   • Click Post or Process

On the Receipts or Payment windows, the Deposit / Prepayment field is missing