I did the couple's match, and have to say that it is run very well--better that the NRMP's version.
It's as the others have said; you submit your list as usual, but you will supply a list of your partner's programs as well. SF match will run your match first and then call the geographically relevant programs on your partner's list. So in fact, your partners list doesn't have to be ranked by preference--it's probably easier for the SF match if it's ordered by geography.
You will then get a call from the SF match--mine came at about 9:30pm about 3 days prior to the actual ophthalmology match date. You are told where you are scheduled to match, and then are told vague details about the phone converstation the SF match had with your partner's programs. It basically amounts to 'high probability, maybe, or don't hold your breath.' With that, you're asked if you want to accept YOUR spot, or if you want to move down to your next would-be match and wait for SF match to call more programs.
A difficult scenario is if you were matched at a great program, but were, say #6 of 6. In this case, even if you accept, you could imagine that in this musical chairs game, you might get bumped out of your spot. You'd be told if this were a distinct possibility--but I can't give you any more useful advice on the matter because thankfully I didn't go through it.
In the end, it's all unofficial since SF match and NRMP are sort of enemies. You'll be told that nothing is documented about SF match's conversations with NRMP programs, and that a lot of it is based on trust rather than contract.
The benefit of this system is that I think you have more control over the situation. Being able to actively make the decision is nice. I believe the NRMP system lets you rank combinations, but to me, it's not the same--guess I'm a control freak. Go figure.
Hope this helped.