There is no ability to automatically add a credit card surcharge. Instead you can use a discount item and set the discount rate as the surcharge %.
The discount would then go above the invoice lines. A discount item also
takes GST into account.
If you are already using discounts the other option would be a separate
line item on the transaction.
We generally wouldn't use payment discounts (on the accept customer payment
window) for credit card surcharges as this type of discount has no GST
The only other alternative I can suggest would be a having a script developed if you
need this task automated.