You use a Service item on a Sales receipt; this is linked to Income or to Liability, to meet your accounting and tracking requirements. That way, everything has each customer name on it, and that Item (product/Service) for reporting and for handling taxable treatment.

Y0ou don't use Banking deposit and you don't post as AR or use Receive Payment. All of this is negative AR. The receipt of this money either is your Income or your Liability, and never negative AR under proper accounting for having the funds on hand.

Later, you can use your same Prepayment Service on a credit memo for the customer for the date of the actual invoice for full charges, to apply their prepayment to the actual total sale, and reduce that to a Balance Due, for that date of the invoice and the credit memo.