Does not matter if it is QB online ir desktop, the procedure is exactly same, correct and up to date.

1. Sell item for $100

2. Record received payment of $100 posted to Undeposited Funds

3. Create deposit selecting the $100 item (or all that are in one deposit as is case with Square)

4. Add line item negative processing fee for $3

5. Save net deposit of $97

6. Accept green match

Works every time AND IS proper and accepted accounting