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.)