For both the national and regional rail passes, what you actually buy before departure is not the pass itself, but an Exchange Order; you can turn this in for the real thing once in Japan. Exchange orders are valid for three months from the date of issue, so only purchase one less than three months before you plan to start travelling by rail. When purchasing the exchange order, you should also receive a guide to using the pass and a timetable of main rail services in Japan. If not, JNTO offices have supplies of both.

HOW AND WHERE TO TURN IN THE EXCHANGE ORDER
Once in Japan, take your exchange order to any JR Travel Service Center authorized to handle the Japan Rail Pass. The most obvious ones are at the JR stations in Narita (Tokyo) and Kansai (Osaka) airports. Major JR stations such as Tokyo, Nagoya, Kyoto, Osaka, Shin-Osaka, Sapporo and Hakata have travel service centres, but it's often easiest to sort your pass out at the airport offices, even if you're not going to start travelling immediately. At the time of exchange JR staff will ask to see your passport to check that you have been admitted on 'temporary visitor' status. You'll also be asked to specify the day you want to start using the pass; this can be any day within one month of the day you turn in the exchange order. Once a date has been stamped on the rail pass it cannot be changed. JR will not replace lost passes.

HOW TO USE THE RAIL PASS
Once you've received the pass, all you do is show it whenever you pass a ticket barrier and JR staff will wave you through. Since the pass is not computerized it cannot be fed through automatic wickets but this is not a problem as there is always a staff member around.
Seat reservations are not necessary as you can just turn up for any train and sit in the unreserved carriages. However, on some trains, and at certain times of the year, it's a good idea to make a reservation in order to guarantee a seat if the unreserved carriages are full. Since rail-pass holders can make any number of seat reservations for free it's worth doing so in any case.
A few JR trains run on sections of track owned by private companies. Rail-pass holders are supposed to pay a supplement for the section of journey over non-JR track. In practice, you will only have to pay if a conductor is checking tickets at the time the train is running along the non-JR track. Any instances where this occurs are referenced in the route guides.