It's on the eastern side of the park near Mono Lake.
This area is less crowded than the other side and has many more opportunities for accommodations. We specifically stayed at the Reverse River Cabins, which were wonderful, but not particularly cheap. Keep in mind that everything around Yosemite is pretty expensive and accommodations fill up fast.
I would NOT stay in Yosemite Valley. It's like Disneyland in there. We did a quick drive through and I couldn't wait to get away from the area with the hotels and campgrounds.
I'm not a hiker, so can't help you there. But I can highly recommend this product:
http://www.yosemite-tours.org
This guy has put together a series of self-guided auto tours that you download and listen to as you travel around the park. They are full of history, information on the flora and fauna and he will guide you to some of the lesser known hiking areas. They are inexpensive, but well worth the cost. Lots of fun.