Kansai to Naoshima

Hi there,

Yes you can use JR-Pass to travel all the way to Naoshima, except for the ferry of course :)
The island can be reached both from Uno a Takamatsu. There is not much difference in travel time between them but maybe Uno is easier because it is on the mainland of Japan.
Here is the route from Kansai AIrport to Uno and here to Takamatsu. Also see the Wikitravel page for additional information. You can make seat reservations for most of the route.

Activating your JR-Pass is very easy, on the Airport just follow the sights with trains this way. There you will find the JR ticket office. Just hand over your voucher and show your passport to obtain the JR-Pass!

Hope this helps,
Daniel

PS: Mari I hope you don't mind me stealing your answer, feel free to add anything you like!