I am having the exact same problem as the OP. Is it pointless to have square sync with quickbooks if we already have a bank account synced with QuickBooks that the deposits from square are going into?

By having both of these systems synced into quick books, it is duplicating sales which cause incorrect inflation of sales on the profit and loss reports. The deposits into the bank account are categorized as sales and the sales from square sync are categorized as Square Sales, which is causing duplication. With the option to confirm a "match" between the transitions as they pop up the next day to categorized, this doesn't change the report. 

I am not sure if the OP had his question answered correctly, but after reading over the responses to his question, I was not able to find an appropriate answer. So I guess the question is, if we have a bank account synced to quickbooks, should we not have square synced as well?