We had a similar situation on our trip in October 2006: my husband and I were in one room and our two daughters and my younger sister were in the second room. The CM at check-in suggested that we list one parent in EACH room, so that we would have all of the dining credits available on parent cards. We did, and it worked great for keeping track of all of the credits. Only once did we have to use both cards at one meal.
The only problem we had was remembering that my key unlocked the girls' room, not the one I shared with my husband. This was no big deal since our rooms were connecting.