Interest payment - no idea where to begin

Here is what happened:
We received a payment from a customer (insurance company, very large) and they automatically included a small amount of interest for a late fee.  The payment itself is less than the invoice amount, so when we posted the payment including the interest it was still less than the invoice amount.  Then a month later they paid the balance of the invoice but we had applied the interest payment originally and so now the second payment is OVER equal to the amount of the interest from the first payment.

Yikes, let's try this:

Invoice - $100
Payment #1 - $90 + $1 interest ($91)