Square offers free multi-location management features, including linked locations and transfer options, per-location item libraries, device management for security, and premium multi-location reports.
Because of this feature, you will need to select the Square account associated with each of your locations, for accounts that have more than one location under Setup > Company.
When you first configure Square, (and you have more than one location) you will see a pop-up box asking you to select the Square account for each location. You can select the same Square account for each location. Once that is complete, you are done!