I went through the couples match and my advice is this: know your priorities. Would you rather be together at your last choice program or apart at your top choice?
My girlfriend and I interviewed at 12 and 13 programs, respectively. We ranked them all. If you do the math, that comes out to 181 possible combinations. What fun that was.
We were fortunate in that we had five or six institutions that we both really liked, so we tried to match together at one of those. Below those we ranked those same programs, but without us being together (our desire to be at our top programs trumped our desire to be in the same city). Below those we once again ranked institutions where we would be together, but they were our "second tier" choices. And so on. This is a departure from how most couples make their lists, but it worked for us.
I recommend getting a bunch of notecards and writing down all the possible program combinations that you and your boyfriend might face ranking. After all your interviews, sit down and arrange them into a giant uber-list. I also suggest you both drink heavily during this process. Good luck.