Hi Lee,
In that case, do you have a C&P machine in your shop? If so, here’s what I would do:
- Create a new bank account for your machine provider (e.g. “Card Transactions”)
- When someone pays by card, log the invoice as paid from that bank account
- When the money hits your bank (which would be the invoice total minus the fees), tag it as a transfer from your card bank account
- You should be left with a small amount in the card account which would be the transaction fees - you would tag these to another invoice to the card provider, to the category “Bank Charges”
Hope that makes sense 
[Edit]
Take a look at this topic on how to handle card transactions and accounting for fees
http://community.quickfile.co.uk/t/handling-payments-from-merchant-accounts/8865