I've got some information to help you clear things up about the credit card payment processing fees, @mariah353.

You're correct that QuickBooks Payments will charge you 2.99% based on the total invoice amount. Thus, it will not accurately match the service fee item you'll be included in the invoice.

In the meantime, I suggest utilizing a third-party payment processor that allows you to receive credit card payments for free with QuickBooks Online invoices. You can visit the QuickBooks App Store to find apps that integrate with the program. You may also look outside of the program if necessary.

For further information about the payment rates, please visit this resource: Standard Payment Fees & Rates.

Additionally, you can read through this article that helps you learn more about the turnaround time to get your customer payments in your bank account: Find out when QuickBooks Payments deposit customer payments.

Get back if there's anything else you want to clarify with payments by leaving a comment below.  I'll be sure to get back to you promptly. Keep safe!