I appreciate for posting here in the Community. I'm here to assist you with your concern about the customer credit card payments in QuickBooks Online.
I'm personally taking note of your request regarding having an option to add the fee during the payment processing to save time. In the meantime, you can record the fees manually when making a deposit from Undeposited Funds.
Here are some screenshots for your visual guidance:
To stay up to date to new features and options, I also recommend visiting our QuickBooks Blog website.
Feel free to reach out to me for any additional questions or concerns about the fees. The Community will keep an eye out on your response.