Payment Plans with previous payment?

We've got a tricky situation with our payment plans for new subscriptions, and I'm a bit perplexed.

We began our subscription campaign about a month ago selling into dummy performances. Now we've completed our season setup and have rolled over all subscribers into real subscription packages. We're working through the orders that had previously been paid by returning the dummy tickets and applying the monies (via an on account payment method) to the actual subscription order. 

Our problem comes with orders that only have a partial payment. After applying the money from the partial payment to the subscription order, we still need to set up a payment plan for the remaining amount. However, payment plans seem to want to be made for the entire amount of the the order rather than for the remaining total. When a schedule is set up for an order where the total due is less than the order total, we get an error message saying "Schedule Does Not Match Total Due."

I found this note in the documentation on Payment Schedules:

NOTE: Payments already made on the order are not considered in scheduling installment payments.

So it sounds like this is the expected behavior... but I can't see why. Regardless, has anyone faced this scenario before? Any thoughts or words of advice would be greatly appreciated.

Thanks,

-Brian