I'd love to know too. I use Square as my point of Sale for CC but would like to invoice etc. through Quickbooks. I set up the Square/Quickbooks Sync App and received my first payment last night. In Quickbooks, the payment shows up as a separate paid invoice and if I were to mark the Quickbooks invoice as paid, my account would register as if I had been paid twice for the same invoice. I would like to know how to take that payment in Square and apply it against an invoice in Quickbooks so that they are reconciled and the payment matched with the correct invoice.