When we first started with Stacker Classic, I had different apps for different departments. It was a nightmare. Correspondence between departments was impossible and when I would change the layout in one app, I would have to remember to do it in the other. Also, managers would have to switch between apps and remember which was which.
With StackerX, I set up unique roles for each department. In my layouts, I use tabs for different workflows or sets of information, then set up role visibility on entire tabs or certain sections or on specific actions. The nice thing is that two different departments can talk to each other about the same record (under "Activity") but only see the fields/actions applicable to them. Also, managers can see everything they need to in one place.
I hope that helps! If you have specific follow-up questions, please let me know :)