For the manual payment option, you could just select check and then type in a description of CASH 2016-02-18 or something similar for the Check Number. This should work how you are describing. I created a PO for 160,000 with a prepayment type of manual payment and amount of 5,000. It debited the prepayment account for the $5,000.00. I received the items and then entered the invoice through Enter/Match and it recognizes the prepayment and credits the prepayment account for the $5,000.00 and AP gets credited for the $155,000.00.
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