Well how about a couple of Questions first.
What scale will you be modeling in?
What Era and basic Theme are you leaning towards?
Do you like operating a railroad like a real prototype or are you more into having a place to show off your models?
Right off the bat i can advise a couple things.
#1- avoid duckunders.......Just say no!!!
#2-Shelf style where you can reach everything easily for maintenance,cleaning,repairs etc will give you far more enjoyment and less strains and pains.
#3- make your aisles comfortable and make use of backdrops as scene dividers.
#4-just because you have a 12' x 12' area to use, doesnt mean you need to fill it with benchwork. Depending on your scale , a very nice railroad can be modeled in a lot less square footage.
#5- consider building this in modules.You gain alot of experiance as you build each one and the layout becomes portable enough that it can move with you should the need arise.(divorces and job changes have killed many a model railroad that was not portable)
Thats a start, i'm sure i'll come up with lots more.
