The web page for the Connect to Square App says it supports multiple locations. It does indeed do this with separate settings for each location. I'm not sure why no one can tell me how to get QBO/Square to import and why there is no documentation on how to do it. There are videos on setting the app up, but nothing for after the fact. 

Square by Commerce Sync wants $10 per location and I have many locations in Square because we are mobile pop-up. As a result, I use classes in QBO, but that means I have to pay $80 a month for QBO. Now add on $10 a month per location and since we only do 2-3 different locations per month, we are priced out of QBO. $80 for QBO just to use 2 classes is already too high for us.

As a result of these issues and a number of other QBO issues, I'm just going to have to shop for a different accounting software or use a spreadsheet.