The Customer Prepayment form effects four areas. The A/R, a liability account, an item is then created in the Receivables with the amount of the deposit and then that amount is calculated into the balance field in the Customer form.
When you create a Customer Prepayment, the amount that you enter is going to affect the A/R account and a liability account, which in our sample file uses 2-1220, Customer Advanced Deposits. When you post this Customer Prepayment, a file is created in the Receivables for that amount in the form of a negative number, which can be applied to any invoices that this customer has in the future.
To deposit this money into your bank account you would create a Deposit and select the bank account you want to deposit the money into. In the Line Item Detail you would select the 2-1220 liability account or the liability account you used when you created the Customer Prepayment and enter the total in the amount field. This will increase your bank account balance and decrease the liability account you used by that amount.
When the customer decides to purchase an item you can apply the Customer Prepayment to an Invoice, which is done in the Receivables form. Select the same Bank Account you used to deposit the original Customer Prepayment. If the customer has an Invoice for 500.00 and a customer prepayment of -200.00 then enter both those amounts in the Receivables Line Item Detail. When you Post this transaction your bank account will only be increased by the difference of those amounts, which is 300.00, since you already deposited the customer prepayment of 200.00.