I'm in the same boat and still trying to decide. My 4'x8'x10' "L" layout will be a winter display for my wife's Bedford Falls collection of buildings and will have 4 levels with 3 very simple runs for trains. The 1st design would have most of the lower level covered and buildings, etc., on the other levels. The 2nd design would have more of the lower level visible with buildings behind the pylons that support the upper levels. I don't like the Chicago "L" look, so I am leaning toward the 1st design with 3 areas and the shelf for her collection. I probably won't make my decision until after the lower level is built later this year.
In your case, you already have things done that affect the height for another level. If you add level with full decking, you'll cover a lot of your accessories. If you go too low with it, you'll have to redesign your mountain and relocate other items. If you follow Carl's advice you can work around those obstacles with a run on pylons lie the Chicago "L". There are folks who raise the 2nd level high enough so you can still enjoy what's underneath and have a full 2nd level all to itself.
