Good day, Eva2019.

When you receive the bill, you should enter all the details from it to QuickBooks Online. If there is a shipping fee added on the next shipment, you should enter it. If there's another shipping fee on the last one, enter it as well. You don't have to add the fee in a lump sum amount. It might be the reason why you get a negative duty.
 

You can always go back to this thread if you have further questions.