Need basic questions answered please

Hello! My boyfriend and I are arriving in Tokyo on August 21st and are very excited for the trip! I have been looking through threads to help plan our trip (we have 11 days total, leaving September 1st for Philippines) and I just want some feedback about the JR pass and where it would be most effective.
First of all I should mention we already have JR passes, purchased a few weeks ago. As for the itinerary this is what I have so far:
Fly into Narita and using the N'EX Tokyo direct ticket to arrive in Tokyo. Buy a Suica(?) card for two people to use for city transportation. Leave Tokyo the 25th for Hakone.
Hakone for one night. Onsen hopefully!
Takayama for two nights.
Kyoto for either three or four nights, possibly doing day trips to Kobe and Nara.
Leaving Tokyo at 11:45 pm on September 1st.

Now here come the questions:
1- I was thinking of not activating the JR pass until we leave for Hakone or Takayama, for the first option, it would run out the day before we leave the 24th. I have seen this Hakone free pass and am not sure if we would benefit from the purchase or not. If we activated it in takayama, then we would have it for the rest of the trip, when we would be traveling back to Tokyo from Kyoto to catch our flight late late evening. Which option would be most cost-effective as well as good time management?
For example is it better to activate in Hakone, then buy one way tickets from Kyoto and use Suica card in Tokyo for the last day?

Overall, the JR pass is overwhelming me :s what is the Shinkansen? Where do I buy a Suica card? I need a simple, straightforward education on the JR pass and where it goes.

If anyone could help answer some of my questions and ease the anxiety I would be so grateful!
Thanks!
-Tracy