First of all, it would be very helpful to post an example of the kind of look you're going for or a similar shot you're trying to recreate. In animation there are limitless ways of making things so it really helps to be very specific. For now I can advise this much...
1. Render your hills out of your 3D application as an image sequence that supports transperancy if you want to layer them or you want the sky to show up behind them.
2. If you want the train to go around the hills, it really depends on how you make the train. Are you also rendering that in a 3D app?
3. I don't know what you mean by getting the camera to reflect, but when you make a layer 3D, After Effects shows the Material Options settings that allow you to control how your layers react to different lighting setups.
The answer to all your questions is: You can't. Not without plug-ins like Element 3D, AtomKraft or any of that. Of course you can get some interaction using render passes for normals, motion vectors and al lsorts of mattes in 2D and 2.5D, but that, too, requires plug-ins. So for what it's worth: Simply do it in your 3D program all the way.
While AE can certainly be part of a workflow with exchange of 3D data and 2D renders from 3D software, this is certainly not a case of "click the button on the left to get a cool animation."
I'm amazed that you think that such a complex task can be achieved by getting some tips in an online forum. At the same time it is fascinating that our tools have progressed so far that you even consider it.