For now, adding a credit card fee when choosing to pay online isn't possible when you're using the Merchant Services in processing the payment. It's because the credit card processing fees are charged every time you do a transaction.
You'll want to manually add the charge on a separate line item to specify it on your invoice.
On your invoice transaction, click an empty line below the Product/Service column.
Select Add new from the product or service drop-down.
Enter the description of the convenience fee on the Name field.
Click Save and close.
Once done, enter the Rate.
Click Save and Close.
To learn more how credit card processing fee works, please check out these articles: