Is there a way to charge a customer and they pay by credit card and automatically have the cc fee in the invoice but separated for bookkeeping .

Hello there, @lauren37!

You'll have to apply for a QuickBooks Payments account first so you can start accepting payments online. You can read through this article to learn more: Accept payments in QuickBooks.

Lastly, here's an article you can read for ideas about what you can expect after accepting payments: Find out when QuickBooks Payments deposits customer payments.

If there's anything else that I can help you with, let me know in the comments. I'll be here to lend a hand.