Hi there,
Happy to help you with any questions, no problem if they've been asked before.
Now that's out of the way, let's have a look at Hyperdia. The website is a great tool for planning your trip but will take a bit time to get used too.
The additional search options are the key to get the best out of the JR Pass. In general you should make sure that the following options are selected:
Bullet Train (SHINKANSEN)
Limited Express
Express
Liner
Walk
Sleeper Limited Express
Sleeper Express
Local Train
Japan Railway(JR)
These are all covered by the JR Pass. The option NOZOMI / MIZUHO /
HAYABUSA (SHINKANSEN) is a bit tricky. As the Nozomi and Mizuho trains are not included but Hayabusa Shinkansen is included. The Nozomi and Mizuho travel south of Tokyo to Kyoto, Osaka, Hiroshima and Kyushu. Leave this options off if you go to any of these place. However turn this option on when you travel north of Tokyo to Tohoku and Hokkaido.
The Private Railway option should be turned off when searching for the JR Pass. It is still useful for finding routes though, sometimes a station is not served by JR and keeping this off will not show any results. You may then want to turn it on to find the route. It will also tell you how much of a fare is required.
Hope this helps,
Daniel