I you plan to visit also Kyushu island I would suggest to see:
Beppu city - the most famous onsen city in Japan (you can try many kinds of treatment there - onsen, sand bathing, mud bathing, steam bath)
For cheap accommodation in a traditional Japanese house there, google for HAPPY NEKO, BEPPU
Mt. Aso - the biggest active volcano in Japan (accessible by cable car or by hiking trail)
For more information on the places, just google for them.
If you would like to try zen-meditation there check -
zenretreat.com > vitamins for the soul