Hi Mokadoka,
All your Square transactions will be downloaded in QBO, including the fees. Therefore, you won't need to creating anything in QBO. Just be sure that you have the correct mapping an account assignment, so the fees and the deposits will post correctly.
Your invoice will be paid in full, but you will have another transaction for the fee. Then, the net amount will be deposited into your bank account. All these transactions will be exported to QBO.
Please check out the article about syncing with Square. It explains about the setup, the things you need to do in QBO, and the mapping of transactions.
If you have additional questions, you can always go back to this thread.
