To make a seat reservation
, you will have to go to a JR ticket office with your Japan Rail Pass and tell them your itinerary.
The day of your journey, you just have to show the JR Pass at the control gate and find your seat on the train. The car number will help you to find the right place to wait on the platform. Car numbers are indicated on screen and on the platform floor.
Here is how to read your Shinkansen Reservation Ticket :