We use multiple locations to break apart different parts of our business.  We have one location for Retail, One fore Wholesale, and one for our mobile locations.  you can have the same bank account or different bank accounts for each location.  I do this because the retail numbers are useless with the multi-thousand dollar wholesale checkouts, so all the visitor's count and avg ticket and busiest hours etc are totally skewed.  The same would apply if your 2 locations are under one account the data and sales etc are kept separate but easier to manage under one account.

as for payroll, l I don't know how that would work as we have used a Payroll company for years before Square started with theirs.