The JR Pass if for all of Japan. Each area of Japan has a different JR Pass. JR West, JR East, JR Central, etc. The Kansai Area Pass is probably the pass you will want to use....
JR-WEST RAIL PASS
But it also depends a whole lot on how much traveling you are going to do. If it's only for a few short trips here and there, most of the time it best to buy the tickets individually....