Which station to catch Tokaido Shinkansen?

We are heading back to Tokyo after a night in Nikko using World Heritage pass. We are activating our 7 day JR pass and heading to Kyoto. I am having the hardest time figuring out which Station to get the train, we want to take the Hikari since its faster. I know I need to reserve our seats also. Thanks for any help.

You can catch the shinkansen from Tokyo Station. You do NOT have to make seat reservations. They are optional.

If you return from Nikko and continue to Kyoto on the same day, I recommend not to purchase the World Heritage Pass, use a regular ticket to get to Nikko and then use your Japan Rail Pass to travel by shinkansen from Nikko to Kyoto. It will save you time and money.

Just expanding a bit further on what Uji mentioned. The best method is to use the JR lines from Nikko back to Tokyo and then on to Kyoto using your JR Pass.

You will want to catch a JR Nikko line train from JR Nikko station (this is different but close by Tobu Nikko station) to JR Utsunomiya station, then catch a Shinkansen from Utsunomiya to Tokyo Station, then catch an Hikari Shinkansen from Tokyo to Kyoto station.
http://www.japan-guide.com/e/e3805.html

Note that you will need to exchange your voucher for the actual JR Pass before you go to Nikko, as you can't activate a JR Pass in Nikko or Utsunomiya.

If you fly into Narita you can exchange your voucher for the JR pass at the airport. Note that it is perfectly fine to specify an activation date in the future (obviously choose the date you leave Nikko).

Also note that you can start making seat reservations once you have the actual JR Pass, so you could book seats from Utsunomiya to Tokyo and Tokyo to Kyoto while you are at Narita Airport.

You can also exchange your voucher for the JR Pass at other stations/offices as listed here:-
http://japanrailpass.net/eng/en009.html

You can use hyperdia to look up timetables in advance, just un-tick "Private Railway" and "Nozomi" from the search and choose from Nikko to Kyoto.
http://www.hyperdia.com/

It will take roughly five hours.

Enjoy your trip!

Thank you Uji and GC3, I will take your advice. This is helping me feel more confident about what to do since it will be me and my 15 year old daughter! I will make my reservations at airport. What time is a good time to leave Nikko and miss rush hour in Tokyo.

Thank you Uji and GC3, I will take your advice.

No worries!

This is helping me feel more confident about what to do since it will be me and my 15 year old daughter!

I'm sure you will be fine once you are there.

I will make my reservations at airport. What time is a good time to leave Nikko and miss rush hour in Tokyo.

There won't really be any rush hour in Tokyo as you will just be changing platforms in the Shinkansen section of the tracks in Tokyo Station, so it probably doesn't really matter what time you are in Tokyo. Just leave Nikko based on what is comfortable for you to check out, and/or base it on how much you wish to do in Kyoto once you arrive.

Enjoy your trip!