I'll share with you a work around on how add the credit card fee on your invoice. You can add it as a line item on your invoice.
Here's how:
Open your invoice, type in your customer details.
Under the Products/Service column, enter the product/service and on the next line, select Add new.
In the Product/Service information page, choose Non-inventory. You can type "Credit Card Fee" as the Name.
Hover down towards the Income account and then pick the account where you record your fees.
Click Save and close.
After creating a credit card fee line item, you can now include the fee on the invoice. Once your credit card downloaded the transactions, you can then match them to your invoices. For details about the credit card processing, please check this link.