Process invoice payments as a separate transaction or deposit - QBO integration

[supersecret]

I'm working with a shop that uses Square for POS sales and for invoices, and is integrated with QBO. The problem is that for the sales summery and deposits, all the transactions are combined into one, so I need to manually go through, find the items on the summery, remove them, etc etc... its a convoluted process and a total hack job.

Is there any way to get Square to process those deposits separately, with auto deposit set up? Or any other ways anyone has found to separate invoice payments from the rest of the shop receipts? 

[Candlestore · Accepted solution]

@supersecret ;

From my understanding the QBO integration was made and handled by QuickBooks.  

Quickbooks Integration will tell you it is Squares fault for the way the Data from Square is scent and received by the QBO integration.

Now the only way I know to dow what you are requestiong is to look into another integration or setup Zapier with your Square and QBO accounts to see if what your looking for is possible.

I used QuickBooks Desktop and found an integration that I would Manually have to Download Transacations from Square.

I used Excel Power Query to automatically take 2 Downloaded csv files from Square and remormatted Squares Columns and some Quantities.  For example for this to work square shows rhe tax per item and you also need the total tax for the sale to show everything in Quickbooks Desktop.I used Transaction Pro Importer for Desktop but there is also a version for QBO.  I believe you should be ab;e to setup a Customer sale with Line items for each Sale (transaction ) in Quickbooks using the TPI program.  It is now offered through Right Networks I believe.