Applying installment payments to inventory receipts

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We have a contract with a vendor to receive several different products on an as needed basis. We are paying the contract in installments and not per shipment, so they send us a quarterly invoice for the installment payment and a $0 invoice noting the shipped quantities after we receive a shipment. My problem is that I am not able to find a way to apply the installment payments to the purchase order or the shipment receipts. The only way I can think to do it is to create a non-inventory invoice to generate the installment payment and then void that invoice after I have received enough shipment receipts to match the installment payment total, and reapply the installment payment to those receipts. Does anyone know of an easier way?

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