I agree it's best to stay in the park if you can. We stayed at a lodge outside Midpines and it was a long drive every day from there to Yosemite and back. Plus there were some long waits at times due to a rockfall cutting off one of the roads.

If I were to go back I'd love to stay at the the Ahwahnee. We lunched there and it was very atmospheric and loved the decor. As you only have two days this would give you a great central location.