Create an AP Voucher for the amount of the pre-payment and process a cheque from the voucher.

Search the archives(Advanced Payment on PO), I know I had this problem, but can't remember what I was advised to do, but it worked
 
Ragine

I know I have posted this before but I tried a search on several keywords and came up empty so here it is again.  And for future searches - ADVANCE PAYMENT or PREPAYMENT or DEPOSIT on PURCHASE ORDER.
 
1.  Create a type N part number called prepayment.
2.  Add 2 lines to the purchase order, one for a positive quantity and one for a negative quantity of prepayment for the amount of the deposit so the net total of the PO is unchanged.
3.  Receive the positive line, process through AP and cut a check using a dummy vendor invoice number.
4.  When the actual parts are received, receive the parts and the negative deposit line so the correct net balance due passes to AP for payment.

P.S.  We have started a folder for Forum notes and save the print page on relevant issues/discussions so that we can refer to them easily in the future.

Not less effort but it ensures the prepayment is associated with the PO and you don't pay in full when the parts are received.  Paying by voucher retains no record on the PO or with the vendor that you have prepaid against the parts.