Hi! You should include your requests on your reservation (you can include them at any time with a phone call). At check-in, your room will have already been assigned (I understand it's made a couple of days before arrival), so any requests should be on the reservation by then. Don't wait till check-in!
If you'd like a specific building, you should request it instead of just the section (i.e. request "Jamaica Building 45" if that's the building you would like, instead of just "Jamaica"). Remember to put your requests in order of preference. As you may know, there's no guarantee they'll get you any of your requests, but they do try.
From what I understand, if you do online check-in it's very hard to change your room
if you didn't get your requests (the process is already completed). If you check-in at the front desk and don't get your requests, the CM has a better chance of moving you (since check-in is 'in progress', not completed).
In any case, do what's convenient for you. After all, you'll already be at Disney!
