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A great resource to learn about the recommended speaker layouts for 5.1 and 7.1 systems can be found at the Dolby
website. While it's true that very few movies actually have 7.1 soundtracks, the fact is that speaker wire is cheap, and there's no drywall up yet. I would definitely run some wires in the walls/ceilings for the extra two channels, even if you don't make good use of them yet. You can simply leave some wire coiled up in the walls (remember where they are) or to be really neat and fancy, you can put in an electrical box with a blank cover plate. Oh, and if you can, run at least 14 gauge wire, 12 if you can find a good deal. Monoprice
is your friend here. They have great prices on all kinds of wire/cable.
As for your speakers, most folks here would probably recommend avoiding in-wall or in-ceiling speakers unless it's absolutely necessary. Not only is the installation more involved, but upgrading becomes more difficult and most will agree that they won't perform as well as similarly priced "regular" speakers.
As per the Dolby recommendation, for a 5.1 system, the surround speakers should actually be placed on the sides of the room - only slightly behind the prime listening postion (conveniently enough, these will work for a 7.1 system, too). They should be slightly above ear level, but not too high. I think if the lower part of your ceiling is still 7' high you should be fine. Surrounds are commonly placed about 5-6 feet from the floor.
Since the back of your room would be open, for the 7.1 rear speakers you'd need to consider ceiling mounts (unless you go in-ceiling).
I think placing your mains may be a bit tricker, actually. The closets you mention are probably right where you'd ideally place the front speakers. For a room this size, it's nice to try and widen the front soundstage a bit. I could see some monitor-sized fronts on stands, perhaps in the corners, toed into the middle a bit, but you may not want them too close to the corners.
The only other thing I can think of is to try to insulate around the air ducts as much as possible. I have a basement theater and unfortunately, the AC is a bit louder than I'd like it to be.
Good luck - it's a fantastic feeling when it all comes together and you sit down for that first movie.