How to use Application Rule Set

My company uses Lines First - Tax After.  This is causing an issue when customers short pays an invoice and the collectors miscommunicates to the customer that they did not pay tax and/or freight. Our company has two needs:

1. Allow customers to short pay because they dispute a tax or freight amount. And we can quickly identify they are

2. If a customer short pays an invoice and there is no dispute, then we can allocate the payment to the line, tax, and freight.

I know that the second request can be handled by changing the Application Rule Set to Prorate, but it will not accommodate first need. Any suggestions would be helpful to reduce the manual workload and inproper communication of our staff.