Closing Invoice with prepayment

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Hi everyone, hope someone can help me with my situation. I don't have any problem closing transaction (invoice) as long as the prepayment and the invoice amount are equal. Here's my problem,  My customer paid in advance for their order and I recorded it as prepayment. But we are unable to ship the order completely, in 3 mos the shipment will be complete. I already have the 1st invoice but unsure on how to close it in Sage since it's not equal to the prepayment amount. I don't want to wait until we can complete the order to close this. Can someone help. thanks in advance.!