I believe I'm having the same problem. So I create an invoice in QB, and then type in 'custom amount' in square equal to the invoice total- and charge the customer like that. Then I click paid by square on the QB invoice and select the account square deposits to in the drop down box on my QB invoice. However it still doesn't link the square charge to my QB invoice. I end up having a square invoice and a quickbooks invoice in my sales history, both equal to the same amount. Which is 'doubling' my visual profits. Which means most of quickbooks other features are irrelevant since my numbers in QB are incorrect.  Does anyone know how to fix this? Or since we create the invoices in QB instead of square will it always be separate and therefore incorrect?