You can build one deck above or below another. Vertical spacing based on depth of shelf and how much space you want. Do you want to connect both decks and run a train from one to the other? If so, you need a long enough run to make a gentle grade to take the train from one level to the other. Some do this all in the open, say around the walls of a basement, some do it with a helix hidden in a corner or at the end of a peninsula. If you have sidings on this grade, make them level so cars don't roll away.
I just operated on a railroad that had two levels about 24" apart. The grade was so long and gentle you did not realize there was a grade.