I doubt you can put any kind of room location request in when doing online checkin. They usually ask if you want to be near transportation or elevators but that is about it.
You are much better off calling Disney and having any request put on your reservation now.
As already mentioned, in order to be near buses, food court and the main pool, you need to have booked a preferred room. So, you will most likely have booked a standard room. My favorite standard area is 60's, bldg 4, top floor, facing the lake. It's about a 4 min walk to the food court and buses. About 3 mins to the pool area.
50's is also a nice area, as long as you are away from the pool. The rooms facing the pools can be loud. I also enjoyed being way over to the side in the Rubiks Cube area...a bit longer of a walk to the food court, but not too bad, and the computer pool is right there.
I'm one of the few people that doesn't care for a preferred room. We had a ground level preferred room and I hated it. There was a ton of foot traffic going to and from the bus area, as well as the food court area.