You’re doing it right, @stephanie52. 

You’ll have to receive the payment with the full amount first. 

Here’s how:

1. Click the +New icon and select Receive Payment under Customers.
2. Select the customer and enter all the information needed. 
3. In the Deposit to drop-down, select Undeposited Fund.
4. Click on Save and Close once you’re done. 

Check this article for more information: How to Use the Undeposited Funds Account to Receive Payments in QuickBooks Online. 

Once done, you can now create a bank deposit, then add a line item in the deposit window and enter a negative amount for the bank fees.

Let me know if you have any other questions about recording the bank fees. I'll be happy to help you out.