@EmilyW_Tacoma What you describe is pretty complex, and there are a variety of approaches you could take. Here’s a couple that come to mind...
If you want to keep everything in a single course, you’ll need to make it one course for each department, adjusting the training materials as needed. You’d need to add that course to a catalog that is assigned to that department’s branch.
You can also build multiple courses, one training material per course, and then build department-specific learning plans, which are again assigned to the department’s branch.
There may be page/menu implications, depending on how the rest of your platform is built.
As for knowing who HASN’T completed the course, the best way is to enroll everyone who needs to take the course, and then build your reporting to show all course statuses. Those who remain in an “enrolled” or “subscribed” status are those who haven’t taken the training.
Many of the topics that I deal with have small variances by audience. Generally what I get from my IDDs are separate training materials by audience, or, a single training material that goes to multiple audiences. But my reporting must always be by audience. I use things like the course title, code, or maybe category, to “associate” those courses to each other to make it easier to find in Course Management in the future. For example, “Topic 1 for Sales Agents”, “Topic 1 for Care Agents”, etc.
Good luck!