If you are charging credit card fees for customers paying by credit card, you will need to add the fee to the invoice before processing payment.
Currently the system is unable to automatically add a % fee to the invoice, however the work-around for this is the below steps:
1. Firstly you will need to create a product for the merchant fee.
Please note: ensure the 'Don't Upd. Qty' toggle is set on Yes and the 'GST Free' toggle is set to Yes.
2. When you are about to process the invoice you will need to calculate how much merchant fee you want to charge, add in the Merchant fee product to the invoice
3. Update the Unit Price to reflect the fee amount to be collected
4. Now you can process the Invoice.