If we do a refund through the Fee Transaction page, will that be noted on the transactions screen or how will we be able to track that?
For us to assist you further, would you please provide us with the screenshot of your Fee Transaction page?
You can see the refund on the all transaction page. In order to track it, there would be an overpayment fee transaction that would contain your overpayment, and then the refunds would be attached to that. If you click the Paid link on the Overpayment fee, then you would see the refund transactions.
Please let us know if this helped or in case of any further queries.