You can organize Users/Passes and Campuses/Buildings/Doors across your company (or across multiple companies) by assigning them to various Departments.
For a typical company, departments might be things like Sales, Marketing, Executive, Accounting, Legal, Production, R&D, IT, Development, Operations, etc.
The Auditor and Manager roles can be restricted to certain Departments, which is useful for allowing certain users to manage day-to-day operations for a particular Department. Restricted Managers can only see Users/Passes associated with their Departments, and can't edit users with anything more advanced than the Door role (though they can still assign Groups to these users). Normally Managers can assign any Group to their users, but Managers restricted to particular departments can only add and remove Groups that have been associated with those Departments (which would have been done by an Admin when they set up the Group)
Example: Jane Doe is given the Manager role but restricted to the Accounting Department. This allows her to create and delete Watchmark accounts for employees who work in Accounting - but she can only manage users who only have the Door role and not delete Admin user Sally Smith (even though Sally is attached to the Accounting Department and does have the Door role). Jane will be able to see Sally and manage which groups she's associated with, but not delete her or change her info/username. Also, Jane could only choose Groups associated with the Accounting Department to assign to her users - if Sally is a member of a Group called Executives which isn't associated with Accounting, then Jane won't be able to remove it from Sally.
Departments are not associated with particular Campuses or Buildings - this is because users in a particular department often need access to facilities spanning multiple locations.
A common use case for departments is when an building owner wants to delegate access to multiple tenants.
Example: Acme Property Managment owns a building and leases it to 2 separate tenant businesses: Jumping Java and Allen's Insurance. Each tenant business wants to manage their own employees, so Acme creates Departments named "Jumping Java" and "Allen's Insurance". Each business needs to control a single door, so one door is attached to the "Jumping Java" department and the other is attached to the "Allen's Insurance" department. Sam owns Jumping Java, so Acme Propert Management grants him Manager access but restricts him to the "Jumping Java" department. Now Sam can create users for all his employees (who will automatically have the "Jumping Java" department, since Sam is a restricted manager). Sam can also only create Groups and Rules for his employees that grant access to the door that's attached to the "Jumping Java" department.