Bumping this because some friends of mine have just admitted they didn't know MCAT registration was available...
You don't have to register until mid-March or so, but they assign your location based on first-come, first-serve with the preferences until a place is full. So the person who picked small test site A on the first day of registration is much more likely to get it than the person who registers with it as a first choice a month later. If you're just registering now, you may want to plan your preferences accordingly.
Does it matter? Only if you want to either avoid a notorious bad site or try to get into a known very good one. Or if you're registering very late.
This isn't as obliging as the SAT, where if you only put down one preference they'll try and squeeze you in. If you only list one preference and it's full, the MCAT people will put you in the nearest empty seat in the general area. Or general state, if you're not trying to get an urban area. If both of your top choices are full, the same thing happens. They're not very nice about it, and even when they screw up (say, randomly assigning ten students from the same Boston college to place four hours away despite open seats in their preferred locations and very early registration) don't magically squeeze you in to your top location.
(Those ten students were told that even though the MCAT people had made the mistake, all they could offer them were the leftover open spots. And then they tried to charge them the transfer fee. At least they eventually waived that.)
Sadly, you won't find out which spot you're at until they send you your ticket, which is six weeks before the exam--around the end of February.
