Reason code

Dear All, we are planning to implement the reason code to our client but we have some doubt to be clear please help us we  have tested some scenario in our DEV system our doubt is as below example customer has paid excess payment invoice value is 400 Rs and Payment received to the bank is 500 now in our books through F-28 accounting entry will follow as below Customer Cr 400 Reason code a/c Cr  100 Bank a/c              Dr  500 but  doubt is if the excess payment happen customer should be credit of Rs 100 should show in the open item of the customer if we implement reason code then it will create mess please advice