@higginsonabby
"Assuming credit card fees are an expense account on the P&L, and you are entering these expenses as negatives, won't it mess up financials?"

Entering as Negative in the Deposit = shows you incurred an Expense.

For those of you familiar with Debits-Credits:
The Deposit to banking is a Debit
The details are Credits
Checks against Checking are Credits
The details here are Debits, such as Debit Banking Fee

So, putting a Negative Detail into your Deposit screen = just created a Debit to that Banking Fee Expense account.