When you exchange your voucher for your JR Pass, you can make all of your reservations then, or you can make them later. When you make a reservation, it is for a seat, and the seat is numbered, just like in buses and planes. A reservation is a guaranteed seat.

If all reserved seats are sold out, then you can ride in the non-reserved sections of the train. If all seats there are taken, you can stand. You can always ride the train even if it is crowded.

There are many shinkansens between Tokyo and Kyoto, so you should be able to get reserved seats. But if not, you can still ride the train, just not in a reserved seat.

If you're flexible with your schedule for the time of these dates, you can very likely book a seat anyhow when you have your JR pass validated. The Hikari train runs every 30 minutes from 6am until 8pm on a departure basis. The journey takes 2 hours 41 or 45 minutes between Tokyo and Kyoto each way.

Timetable of the bullet train:

…jr-central.co.jp/info/timetable/index.html

Please be reminded that you can't take the Nozomi train.

Hi mch2012, I think it's worth pointing out that you can make reservations right up until the train leaves (as long as you still have time to get from the ticket office to the train!) so don't worry too much about making the reservations in advance. When I was travelling on the Shinkansen with my JR pass, I would just go to the ticket office and make a reservation for the next departing train.

Jamie.