Hi NotEnjoyinBooks,
 
Thank you for contacting the Community.
 
To record the fees and match the remaining amount you can create a bank deposit which will show the invoice for the full amount the customer paid, minus the fee.
 
I would first recommend to create the invoice for the full amount the customer actually paid. When you click receive payment make sure the Deposit To account is the Undeposited Funds account (you may need to create this by clicking add new, selecting current assets as account type and Undeposited Funds as Detail Type).
 
I would then recommend creating a chart of account for the Fees if you haven't done so already. To do this click the Accounting tab and then Chart of Accounts. Click New and select Expenses as account detail and whichever detail type matches the transaction the closest (on this occasion this will most likely be bank charges). You can name the account anything you like EG Fees.
 
To create the bank deposit click the + button and click Bank Deposit. You will see the payment the customer paid you, for example the full invoice could be £3,000. Tick this payment so the amount in the top right hand corner shows the full amount. Then on the Add Funds to this deposit section select the Bank Fees chart of account that you created earlier and type in the fee with a minus (-) symbol in front of the number. EG -57.00.
 
The amount of the deposit will now show the amount minus the fee and this can now be matched on the banking screen.
 
Please let me know if there is anything else I can help with. :)