When disney selects your roomates, I believe you do have some questions to fill out to help them in the matching search. I'm trying to recall the process but it's become a little hazy. But, i know they select because of arrival date first. Then I believe they take your questions into consideration, like you said, apartment preference etc..
I signed up for it and was notified the next day or day after. It worked out very well for me. My friend did the CP in spring 08, didn't like the roommate it matched him with, so when he checked in he changed and it was a random draw. It worked out for him then.
I do know that just because they match you up, does not mean you are automatically roommates, rather apartment mates. You could get paired with someone and decide to live in separate rooms. They don't really tell you that.
For example, 3 room apartment, 6 roommates.
A and B show up first and are matched but dont want to be in the same room. A moves into 1, B into 2.
C and D show up and want to be in the same room so they take 3.
that just mean E and F get to decide who goes into 1 and 2.
It could cause for some confusion and I think thats why they don't ever elaborate that you don't have to be in the same room, just apartment. Unless you have a 1 bedroom.