I don't think you're asking too much. Lots of people have built N-scale layouts that featured long mainline runs for passenger trains and industrial switching areas.
But I would recommend that you look into "live frog" turnouts if you're going to be doing a lot of switching. The little "insulated frog" turnouts make by Atlas are easy to get ahold of and install, but leave a lot to be desired in operation. This is especially true if you're wanting to run very small engines (like 0-6-0 steam switchers and even some smaller diesels).
I've not heard of N-scale-specific problems with derailments and couplers. Like I explained in another post, about the only time I have a derailment is when I forget to switch the points on a turnout. And unless the couplers are improperly installed, you shouldn't have any trouble with them. Most N-scale equipment comes with Rapido couplers. And although they don't look like real-life couplers, they do hold pretty tight!
Take your time in the planning process. I had a couple of false starts before I finally got my first "real" one built. Get ahold of model railroading magazines and books to get ideas. Study as many layout plans as you can to see how others figured things out. And if you don't like the way a layout is going after you get started, there's no law that says you can't take it down and start over!
Above all, though, don't get frustrated! This is supposed to be fun!
-Rory