We were lucky enough to get be a flag family during our last stay. It is tough to get. We stayed for 14 days and there was only 1 opening when we checked in! It's really a great experience. The view from the top of the lodge is just breathtaking.
Just be sure and ask as soon as you get there. They'll put a note under your door the night before telling you what time to be in the lobby, for us it was 8am. You also get a little certificate and they allow you plenty of time for picture taking.
As the other poster said, the room choices depend on what you want. We stayed on the 5th floor, courtyard view overlooking the lobby. The room was in the "U" shaped part of the lodge and had a nearly center view of the pool and lake. It was a perfect room for us, but it really depends on what's important to you.
You might want to check the Wilderness Lodge faq thread. It has a ton of information on room choices!