I always have the CM add any room requests at the time of booking, but you can call anytime. Supposedly rooms are assigned about three days out though, so I'd do it soon. If your request is not met at check in, you can ask if another room is available that might be closer to your request and tell them you are willing to wait for it to be ready. Most CMs will try to accommodate you, but some won't. It's just luck of the draw. If room location is important to you, I would not do online check in. The only thing there for you to check is first floor, close to transportation, and if you need a port a crib or a fridge at a Value. Online check in is designed for people who don't care where their room is located. It just speeds up the check in process (most of the time--sometimes online check in line is longer than regular check in). If you may need to talk to a CM about switching your room around then use regular check in.
When we stayed at PORS the requests I had the CM note were first floor, AB buildings 14, 18, or 27. This was before they made those buildings preferred. When we arrived we had been assigned top floor Acadia House. I very politely asked the CM if there was anything available in AB. She went to the back for a few minutes, then came back and offered a first floor room in either AB 18 or 27. We chose the one in building 18 and it was ready. As we were walking down that hallway past the lounge, Boatwrights, and toward the food court the family that had checked in beside of us, was right in front of us. They were fussing among themselves, that they were stuck in the mansions and how the CM checking them in wouldn't even look for a room in AB and just told them that no rooms were available and they had to take what they were assigned. That other room in AB 27 that we were offered would have been perfect for them, but their CM wouldn't even look.