To add to what has been said...
Create a bump or hill.
Place one end of the road spline up on the top of the hill, or up the slope somewhere.
Place the other on the lower part.
Flatten the terrain under the road by using the smooth terrain button in the splines.
This will create a slope based on the profile you have made with the spline.
Move the spline over and repeat, or alternatively like I do place multiple splines and do a multiple smooth terrain functions by clicking each one.
Now about TransDEM.
TransDEM is not free, though it is relatively inexpensive. For about $33 or less, depending upon the Euro versus the Dollar at the time, you get one of the best terrain management programs out there. With TransDEM for example, you can import DEM height information files from the National Geologic Survey National Map Server along with place-able maps and orthographic satellite or even historic or current topographic maps. Once the images are converted, they can be placed in the exact position right on the terrain, even lining up on hills and rivers. Railroad lines are right on, or pretty close to where they should be and everything is ready for route building when the route is exported to Trainz format. You can even go as far as trimming down the route to a few baseboards on each side, and or even place track that is ready for smoothing.
There's a bit of a learning curve, but once you go this route, no pun intended, you will never, ever go back to hand sculpting terrain again, except is a few locations or if needed.
Now regarding the crossings...(which I forgot to include before).
There are two kinds. One has the gates and workings already connected. The blue-stripes are the track which you connect the track to and the other going perpendicular to the tracks is the road crossings. Then there are those with NRC and use ATLS by Boat... These are separate items which can be used to build custom crossings. You'll need to look for ATLS as it's more difficult to explain and place here in this forum post. Once you set one up, they're pretty easy to use and open a whole new world of railroad crossings.
John