Custom edit invoice price for a subscription order

We often receive subscription agents’ orders where the price paid is a little less than the full fee. Because we don’t want the end-user to wait for their order to be processed, our policy has been to adjust the pricing by the necessary amount when the discrepancy is small. We would like this to be something other than a coupon, because it’s not a set percentage, nor a set dollar amount. It might happen that the amounts are $5.26, $2.35, and $3.97, with each order a unique amount.