When you create a Vendor Prepayment, the amount that you enter is going to affect the A/P account and an Asset account, which you can use a Banking account. When you post this Vendor Prepayment, a file is created in the Edit Payables for that amount in the form of a negative number, which can be applied to any invoices that this Vendor has in the future.
When you receive a Bill you can apply the Vendor Prepayment to that Invoice, which is done in the Edit Payables form. Select the same Bank Account you used to pay the original Vendor Prepayment. If the Vendor has an Invoice for 500.00 and a Vendor Prepayment of -200.00 then enter both those amounts in the Edit Payables Line Item Detail. When you Post this Edit Payable your bank account will only be decreased by the difference of those amounts, which is 300.00, since you already deposited the Vendor Deposit of 200.00.