In QB Online, i don't see a way to do Step 4. I see no way to add a line item to this payment at all - how do you do that? 

See below (bolded at my question):

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 - How? 

5. Save net deposit of $97

6. Accept green match

Works every time AND IS proper and accepted accounting. 

I would love do it this way, just don't know how to do step 4 in QBOnline