When I am receiving payments from a customer and the total on the invoice does not match what was paid and I try to go back and change it. When I unclick the invoice, open the invoice and change it the amount due on the payment changes? Why is that?
You should never change that invoice; you just changed a historic Sale. That impacts all financial reporting, and if you are subject to sales tax reporting, that is the worst change to make.
When a Payment doesn't match an invoice, you have to figure out why and act accordingly. Perhaps this is Underpaid now, and another payment will come later. That is no reason to Change the invoice. If they are underpaying as a dispute, and you agree with that dispute, you make a Credit Memo to process that you intend to write off some goods or services or as other charge item, and apply that to the remaining balance of the invoice.
You process the payment for what you got; you don't make the invoice match the payment. The invoice is Your Sale.
The Payment is the banking; so you process that in reality, as well.
If there is a difference, you deal with the difference accordingly.