I put everything (scenery, trains, industries, etc) into the Route Layer. That being said, TANE will automatically put all Driver Command stuff into a/the Session Layer.
I run with just one Session per Route. Many trains, many industries, etc. If my Route is named Big Yard Rte, my Session is named Big Yard Ses. The suffix makes it easier for me to export and import CDPs as I currently develop in 90945 and then also test in the latest Beta.
I always Select Route - Edit Session. Once in Surveyor, I immediately select the Route Layer and all new stuff, including new trains, goes there. But, since I got into Surveyor through Edit Session, when I add Driver Commands, do Quick Drive and Save (both Route & Session), everything stays in sync.