Create a New Payment method in

General Maintenance – Payment method Maintenance

Bank Charge Account assign to Transaction Fee Account

When Received Payment

1. Select Payment Method – BANK- ECOMM
2. Update Invoice total amount Received from E-Commerce
3. Update Transaction fee in Bank Charge Column
4. Knock off Invoice

Double Entry of this transaction

Remark :
if Transaction fee have fixed Percentage , you may setting in Payment method maintenance , it will auto calculate transaction fee in every received payment