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Thanks for the clarification, @absllc.
You'll need to enter an amount after the negative sign to record the bank deposit fees. Entering a negative sign without an amount is not possible in QuickBooks Online (QBO). I've attach a screenshot below for visual reference.
Also, ensure to include the payment in recording a bank deposit for QBO to save the transaction smoothly.
In addition to this, you can check this helpful link that guides you in reconciling your accounts precisely.
You can always tag me in if you have other concerns. I'm more than happy to assist you. Have a great day!