I only get the special request option when booking with my developer points (and we are VIP Founders). I don't have that option when booking with my resale points. It's on the 'complete booking' step. You have to expand the special request section (hit plus) and can enter a room number. I don't have a particular room we prefer, but I do like to face the lake (or a pool).
I also always call before checkin and request a lakeview. I think even just a few days in advance is good enough, although I try to call about 2 weeks prior as a rule. Rooms are pre-assigned by the room controller, and they do take requests from owners (not guests, unless it's handicapped or medically related). Even parking lot views at Bonnet Creek aren't bad, if the rooms are high. I realize the lake is pretty awesome, but if high, it's not a bad view. One of our last stays they upgraded us to a 1 BR Presidential, parking lot (they call conservatory), we could see the fireworks (I think they were Epcot's) . And yes, ultimately up to the room controller gods where you are assigned, you can't book at Bonnet Creek based on tower or view.
I do this almost everywhere we stay unless I have no idea what to ask for. In that case, I may call the resort and ask what they recommend.