You can manage Departments by clicking the employer name in the main menu and choosing Settings -> Departments.
We assign each new department a colour, but you can select your own. You must also provide a name and a code for each department.
Edit the employee and go to their Employment tab.
You will see a Departments section only if you have added at least one department.
From here you can join the employee to one or many departments.
If the employee is assigned to multiple departments then one must be set as the primary department for the employee.
Once you've set department memberships for employees you'll see that various lists can be filtered by departments.
This includes the main list of employees as well as pay run entries.
Various reports will include the Department information once it has been set.
The journal report will give you an option to break it down by department.