Do you have advice for setting up a larger organization? 

In a scenario where you are a larger organization it would make sense to create a separate organization for each site. A site manager would create their account and then could use the Invite A Colleague feature to invite others at that site. Doing so would mean that only those at a particular site would be able to communicate with each other and use the collaborative features. Alternatively, you can have everyone part of the same organization. The best process will depend upon the needs of your particular organization. 

There's more information in our guide for administrators as well.