How to handle excess payment

How can I handle excess payment? Lets say Invoice amount is 100,000.00 with 1% discount.
In normal payment, I will only pay 99,000 and I will use the write-off account wizard for the discount. In this scenario I don't have problem but what if the customers payment for this invoice is 110,000? If I use the same normal procedure and pay only 99,000 as the amount of invoice, then the amount that would go to my discount account is not just 1000 but the amount would be 11,000 which is wrong, 1000 should go to discount account and the 10,000 will go to another account. How will I handle this situation.

thanks,