My personal preference is the Arusha Savannah. I would request a room on either Kudu or Zebra Trail facing Arusha. Although everyone I've ever asked at Disney swears all 3 savannahs are the same size, the other two seem smaller. That being said, I know I've read many posts from people on this board who prefer the other savannahs. There are different animals on each savannah (though there are Giraffe's on all 3). For example, I love Thompson Gazelle's and they were NOT on my savannah. Plenty of places to view all savannah's regardless of which one your room faces.
Sorry - can't help with the bunk bed question!