From experience...and reading a crapload of posts here and there. I havn't got into many question asking as of yet...but I have found some layouts are a certain height and merging them into a route you created at 0 will cause sufficiant height differences...thus needing many a board to merge a gradiant that would look correct...instead of the rollercoaster effect.
The last month I have been working ona ficticious route of around 2000 miles of track, so far have 4 drivers running without assistance and also with 2 passengers passing through every 15 mins...and adding to it you need to be selective as to what will enhance your layout...or so to say make it a longer fun route to run.
All I can say is read up...experiment...hind sight is 20-20 and we are supposed to learn by mistakes.
Also on another note...if you have made a route, and have sessions running when merging two routes select yours first over one that say has no trains in it...or yours will be merged to a layout that has no trains in it...thus youll need to add trains or rolling stock back in.
At least that's what I have had happen...
running TS06 here...
be sure to back up!!!!! before making major changes...I have lost weeks/hours of work...save often