For most of the trains in Japan, booking seat in advance is not required. Travelers can just board the train with their Japan Rail Pass.
As for the Shinkansen (bullet trains), most of them are equipped with 3 non-reserved seats cars (ordinary class) that are available for boarding with only the JR Pass.
However, JR Pass holders can book their seats as well.
Reservation is free (with the countrywide JR Pass) at a ticket counter in Japan. When ordering a JR Pass exchange Voucher with Keikaku, you will receive maps to tickets counters in the biggest train stations in Japan.
It is not possible to book train tickets before departing to Japan (with the exchange Voucher only). You must have exchanged your Voucher for the JR Pass in Japan to be able to book seats.
However, once you get the JR Pass, you can book tickets even if the JRP validity period is not started yet.
Please note that Keikaku doesn’t book train tickets for travelers who are not holding a JR Pass.
Be aware that train tickets in Japan are non-refundable.