I was in a similar situation to yours... the Army GME people (Ms Cox et al) are super, and seem to go to great lengths to get couples stationed together. Of course, with the military, NOTHING is guarunteed, but of the small number of dual-resident couples I know, all of them got into residencies in the same location.
(Shows you how bad I am at statistics if you spot the obvious error in that first paragraph <g>).
Make sure all the programs you interview at know that you will be matching with your SO. You'll be surprised at how PDs talk to each other - my wife is a year ahead of me, and when she was matching, I met the PD of the program I was planning on applying to (later changed my mind, but that's another story) - he had already heard of me from my wife's PD & was watching for me.
As far as residencies of differing duration, it is less of a sure thing that whoever did the shorter residency would get to stay on - probably depends on what the residency was, whether there were non-hospital billets for it at the same location, local policies and "needs of the army".
For instance, if one person was doing FP, AND the army had a slot open at the clinic down the road from the hospital, you might be in luck - I use that example because I know many PDs have a policy that they won't have an attending who is a fresh graduate of the program.
Best advice I can give is to be up front and proactive when talking to Ms Cox, and the PDs for all the programs both of you are applying to. Like I said earlier, the army tries to bend over backwards to make things like that work, you can help by being proactive, but nothing is guarunteed.
