one method

Chris,

One method for double decks is to use an "X" assembly, very similar to picnic table supports.  The top of the "X" supports the upper level (corresponding to the table top), and the lower level is supported by horizontal members that would correspond with the seat supports on the picnic table.  This method puts the legs out of the way of the lower level.

Hope this helps.

And I also have used Suydam kits with success.  They make good background structures, and with additional detail, they can even be in the center of view.  They are now found in the selection from Alpine Models.  Nice folks, great to do business with.     alpinemodels.com/index.html  (and. they're an MRH sponsor)

Suydam (Alpine) Kits

I'm a big fan of those kits for a couple of reasons.  One, they're simply fun kits to build, whether we're talking about the metal solder kits or the cardstock glue together kits.  I've built several of them over the years, starting with the Swift plant about 25 years ago (which my dad recently found in storage, still in decent shape) to the Sunkist Fruit Packing building for my current layout.  The other reason I like them is that they are one of the few kit lines that has buildings that are appropriate for California in the 1960s.  All too often, building either look too modern or too east of the Rockies.  The only drawback is that they're a bit on the small side.  I saw some one kitbashed the Sunkist Packing using two kits and it looked great.  I wish I had done that! 

How wide will the top deck be

How wide will the top deck be ? Modular shelf brackets should work for anything up to about 16" . Especially if you use foam for the decks.....Mike

upper deck support

I build a 2x4 stud wall down the center of the peninsulas. Where the track is at different elevations on each side I support the upper deck as below.

A 2 x 2 and a 1 x 4 are glued and screwed together. The 1 x 4 is screwed to the 2 x 4. The 2 x 2 buts against the stud and is supported additionally by a shelf bracket. This has proven to be very strong.

Where the track is at similar elevations I run the joist all the way across the peninsula and screw it to the stud.As  shown here

Finally where the shelf is very narrow I just screw it to the stud as here

These are not my best photos but I hope they give you some ideas.