Can I set it up to where the customer pays the processing fee with the invoice?

Hi, Clark.

Let me help you with the payment processing fee in QuickBooks Online (QBO). While the program doesn't have an automated way to directly charge your customers for the fee, you have the option to manually include it in their invoices and pass that cost on to them.

First, let's create dedicated service item for the fee. This will allow you to include it along with a detailed description on your invoices. Here's how:

1. Go to the Gear icon.
2. Select Products & services.
3. Click New, then choose Service.
4. Enter the name of the fee item.
5. From the Category dropdown, select the category that best describes the fee.
6. Fill out the rest of the fields.
7. Select Save and close.

Once done, check this article to for more details to learn on how to add service fee to invoices, check out this article below: Manually add service fees to invoices in QuickBooks Online.

In addition, feel free to read these articles to learn how to personalize your sales forms and enter customer payments in QuickBooks Online: 
 

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

Return if you have any further questions concerning your QBO service fee transactions. Have a fantastic day! 

QB Payment doesn't offer such feature. If you are B2B, you can have a 3rd party payment processor with the feature to sync with QB.