You really need to give a length of visit for your trip. Here are some basic tips.
Most likely, the great and powerful JR Pass will help you. Please don't expect a great beam of light to shine on you, and to hear a choir of angels, when the pass is handed to you. There are lots and lots of places where the great and powerful JR Pass has no effect. Those places are mostly placed where there is a lot of tourism. The JR Pass will get you from one location to another, say Tokyo to Kyoto, but when you reach a location, expect to use private transportation to see attractions.
http://www.japan-guide.com/e/e2361.htmlHakone is an example of this.
Visit Hakone from Tokyo, and get a "Hakone Free Pass". The private transportation of the Round Course is not covered by a JR Pass.
http://www.japan-guide.com/e/e5210.htmlhttp://www.japan-guide.com/e/e2358_008.htmlDepending on the length of your JR Pass, you will either get the "Free Area" one which starts at Odawara Station (served by JR), or you will get the one that goes into Tokyo. If your final day of your JR Pass ends up at Odawara Station for Hakone, just get the "Free Area" pass, and then pay the single ticket back to Tokyo.
A JR Pass is expensive, but pays off if you go further than just the Tokyo-Kyoto-Tokyo trip. You have two additional side trips, one to Hiroshima, and another to Nagoya. As far as the JR Pass is concerned, it gets you to Nagoya, and private rail and busses get you to the onsen and the snow monkeys. Since the JR Pass is expensive, you don't necessarily want it active while in Tokyo. The other location is Kyoto, in that most of the attractions are along bus lines, and not train lines.
Count the days that you expect to be out of Tokyo, (Hakone counts as "in Tokyo"). Try to make this 7 days or less, so that you can get a 7 day pass. IF your "Outside Tokyo" ends up 9 or 10 days, think about getting a discount bullet train to Kyoto, and then using the Kyoto bus system to explore before activating your JR Pass.
Many people also plan a visit to Mount Koya, with a temple stay. This is another time when private train lines are used, and the great and powerful JR Pass does not help. There are private line passes to get to Mount Koya, and you may want one of these. If you end up going to Kyoto on a discount Ticket, stick mount Koya next on your trip, and expect to use on of these private passes. Then activate the JR Pass for the rest of the trip.
Another factor for your trip is which airport you are going to fly in and out of. Narita is further away from Tokyo, and can cost some to get to and from. IF you fly in and out of Narita, think about having the JR Pass end on the final day, so that you can use it to ride the NEX (Narita Express) from Tokyo to the airport.
Finally, you do not mention Takayama as a possible place. There is a very nice spring festival in Takayama mid April, and I would suggest going to it. You can get to it -via- a JR Pass, but it is also possible to take a highway bus from either Tokyo or Kyoto. It is also possible to not get the single discount ticket from Tokyo to Kyoto, and get the two highway bus ticket to Takayama, and spend a few days there on your trip. This also extends your time without a JR Pass outside of Tokyo.
http://www.japan-guide.com/e/e5900.htmlhttps://www.nouhibus.co.jp/english/Besides the highway busses into Takayama, there are links to the tour busses from Takayama on the Nohi bus link.
This will get you started.
Good Luck, in planning your trip.