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incoming payment question. Bank deducts bank fee from customer amount instead of showing it on a separate line. Is there an easy way to register customer payment and bank fee in one step?

Not without script.

Typical way I do this is to use the Undeposited Funds account to receive payment in full - and then on the make deposits step I pull out the Fee.

Alternate options: Have a custom field with a script that creates deposit record for you and fills out the cash back tab of your deposit transaction for you with the cash back tab filled out correctly or creates a journal entry.