Hi Tanya,
It is a little hard to give you the best available option right now because your itinerary is still in an early phase. I can however give you some pointers that hopefully are helpful when you finalize your plans.
Kyoto is a great city to go too, even if you go for a longer time. You can also reach other nice places from there like Nara, Uji, Osaka and the like. Beppu is very nice to visit too but I would not stay there for a week, unless many you are visiting friends there. The town is best visited as a 1-2 nights stay, it is rather small so you may end up beeing bored if you stay (much) longer. Kyushu the part in Japan is located makes for many nice trips however. What you can do is make your base in one of the central cities like Fukuoka or Kumamoto and makes day trips from there all over Kyushu, such as Nagasaki, Kagoshima, Mount Aso and the like.
On the topic of what pass to get, this is hard to say now but you will be able to make great use of a JR Pass with your trip to Kyoto and down to Kyushu.I would recommend a 21-day JR Pass over getting the 7day JR Pass x 2, if you plan to travel around relaxed and freely. This because the price of the 21 JR Pass (57,700Yen) is about the same as the 2x7day pass option (28,300 x 2 = 56,600) and you get a full week of extra use with the 21 day JR Pass option.
Hope this helps,
Daniel
