I read this on another board...hope it helps.
I recommend you purchase the cruiseline transfer (Carnival didn't charge for this, but Celebrity did). Carnival had us pre-check-in at the San Diego pier and bussed us from there. We were assigned a number (by what time you arrived at the San Diego pier) and boarded the busses by number. There was a nice shopping village a short walk from the San Diego pier and we checked our baggage in San Diego. Our luggage was bussed separately. Busses with passengers didn't start leaving for Ensenada until about 4:00ish p.m. You really won't find out the exact details until you receive your docs and the detailed instructions for checking in are in those. The San Diego pier is not far from the airport.
I'm not certain if RCCL would do it the same way, but I have a feeling it does. The airport seems too congested with non-cruise passengers to be bussing passengers to Ensenada from there.
My biggest tip is to be patient! We have embarked and disembarked from Ensenada and both experiences were very looooooong. I would not fly the same day as embarking just to be safe and stay overnight in San Diego near the pier (fly in a day earlier if leaving from Ensenada) - this way you are there no matter what time the busses start leaving.