Thanks for getting back to us, kaneika.
I've read the replies on your concern and thought a way to fix this. Before we proceed to the troubleshooting steps, I'd like to clarify a few things. When following the steps provided by Angelyn_T, how did you enter the amount for square fees? Did you enter it as a negative or positive amount? Did the original invoice amounts decrease or increase? In what page did you see the credits? When you recorded the invoice payments, were they deposited directly to the bank account or to the Undeposited Funds account?
Additional details about this would be much appreciated so we can provide you the exact way of correcting the transactions.