Well, after laying all the track, scenery, signals, etc. in my route, I start the session phase, using Create Session from the menu. There I place locos, rolling stock, program the signals (I use the GrahamSea ones) and place any industry not specifically included in the route itself in the session-layer. Finally, I make up the commands to get everything going. After that point, any editing I do is of the session, not the route, and I generally add stuff to the session-layer rather than the route as well. That way, if I go to make another session, I don't have any unneeded extras from the previous one. If you have any specific questions, I'm sure you'll get an answer promptly enough (although you might want to ask in the Surveyors forum.)