I may be wrong but when you start working on a route and exit it will ask you to create a new route and session.
Now when you go back and work on your route(not session)and go to exit, it will ask you if you want to create a new route & session or overwrite your route, create a new session, or do not save the session.
Now when I work on my routes and exit I overwrite the route and check the button that ask do not save session. (we already have a session and don't want to change it at this time)
Track, building, landscaping, and INDs can be done it the route.(naming the INDs too) setting up the INDs should be done in the session along with adding rules, drivers, drivers commands,
and adding rolling stock.
Now I only wish there was a list of drivers commands and what they mean along with rules and what they mean and how to use them.