Here are a hodge-podge of additional ideas...
[1] See a fairly current thread, "distance between levels" (http://cs.trains.com/trccs/forums/t/154558.aspx) for a lot of common sense considerations.
[2] Kalmbach's "Designing and Building Multi-Deck Railroads" (http://kalmbachcatalog.stores.yahoo.net/12434.html) @ $19.95.
[3] PDF Download "Guide to helix and staging design" (http://kalmbachcatalog.stores.yahoo.net/mrpdf032.html) @ $8.95.
[4] PDF Download "Guide to helix and staging design vol. 2" (http://kalmbachcatalog.stores.yahoo.net/mrpdf049.html) @ $8.95.
[5] Will benchwork be "free-standing" or attached to the walls?
[6] Will you have a helix or a nolix?
[7] Is your room large enough to employ a peninsula? ...that may even be a location for a helix? See the July 2009 Model Railroader, pages 54-57, for the First Prize, Track Plan Contest, and John Koukol's Maine Central rendering of "A double-deck N scale track plan."
My hunch is you will find, not much can replace the strength of wood/plywood benchwork as a base, and; especially so for a helix. Foam can be placed on top of a solid core of benchwork for its scenery & trackage base plus carving characteristics.
There are many possibilities, but you must first take your good 'ole time with research and planning.