If you're talking about a specific section, such as the Cabanas at Coronado vs the Casitas or Ranchos, or Alligator Bayou at POR as opposed to Magnolia, etc, you can tell them on the phone when you book your reservation, of that preference. To cover their own behinds, they will tell you that they can't guarantee that, but they will make a note of it on the reservation. When we stayed at POR, we requested Magnolia Bend and got it both times.
However, when we stayed at Coronado Springs this past April, I made no request regarding which section and when we checked in, they didn't ask. We were just randomly assigned an available room in the Casitas.
So getting back to your question, from my personal experience, it seems that if you don't make any specific requests, they just randomly assign you a room in a random section of the resort. And, of course, as a previous poster stated, rooms that cost more, such as particular views, King beds, or whatever, you have to request that...or, perhaps request NOT to have it, if they are trying to "sneak" in a higher price room to make the resort more money. I'm not saying they do that, but in previous times when I have booked, when they give me the total, they include vacation insurance, which I did NOT ask for, to which I have to reply that I don't want it. And when I booked the current trip we are planning, they defaulted to the Deluxe Dining Plan even though I only want the regular. So it wouldn't surprise me any if they tried to sneak in a higher priced room and leave it up to you to specify the cheaper one.