Charging a usage fee for credit cards

QB Payment doesn't offer such feature yet. You need to have a 3rd party payment processor to do so. If you are running a B2B company, you can utilize one of them for free.

It's such a great idea to automatically apply fees for credit card payments in QuickBooks Online, @Jstringer.

The desired functionality is currently unavailable in QBO. You can manually include service charges on invoices instead. Before doing so, make sure to create a service fee item so you can add a fee with details to the invoices. Here's how to add fees:

1. Open the Get paid & pay or Sales menu, then click on Invoices (Take me there).​
2. Pick the invoice you like to add a service fee to.
3. Click on Edit invoice.
4. Go to the Product or service, and choose the service fee you created.
5. (Optional) Go to the Amount field, and fill in the amount of the service fee.
6. (Optional) Go to the Note to customer section, and enter a note about the fee.
7. Once done, click on Review and send.

Additionally, I agree with Fiat Lux - Asia to visit the Intuit Marketplace and browse for a third-party payment processor that's capable of charging fees for CC payments to invoices. 

I'm adding these articles that you may find helpful when personalizing invoices and handling customer payments.

• Customize invoices, estimates, and sales receipts in QuickBooks Online
• Record invoice payments in QuickBooks Online

Please let us know how this goes. We're available 24/7 to back you up regarding invoice payments or QuickBooks. Take care!