Hi there!
Not a problem - it can be a little unusual at first.
In Japan on some fast trains like the bullet train, they charge a general base charge, and then an additional charge depending on your seat class and whether it is reserved or unreserved seating. Essentially it's all itemised (I'm not sure why!). Some trains are reserved seating only - the main one you should encounter being the Narita Express.
As a Japan Rail Pass holder you can travel reserved or non-reserved totally for free within your JR Pass class. For example if you purchase a Standard class JR Pass, you will be able to travel by non-reserved and reserved standard class seats.
In practice, this means that if you have time at the station, or the train is reserved seating only, you should go to the ticket window and reserve your seats. If you don't have time, you normally can just jump on the next train and sit in non-reserved. Reserved seats can be good in rush hour times too, but this tends not to be an issue on the bullet trains.
As an alternative way of ensuring you always have seats, you can reserve all your seats in advance when you activate your JR Pass if you know the time and dates of your travel. Simply take your itinerary to a JR desk and they should be happy to reserve all your seats at once.
If you miss a reserved seat you can always hop on the next train, or go and reserve another seat.
Hope this helps!
