Hello @absllc,
Yes, any amount entered in the line item of a deposit even if it is an expense account will add up to the total amount of the transaction. You'll want to enter the fees as a negative amount and select the correct expense account so it won't add up to the total amount of the deposit.
Lastly, here's an article you can read to learn more about your account and related tasks: Reports and Accounting for QuickBooks Online.
If there's anything else that I can help you with, let me know in the comments. I'll be here to help.
