Ticket offices of JR groups are called as MIDORI NO MADOGUCHI in Japanese. Midori means green and madoguchi means window.
Actually almost all Japanese do not know why the ticket office was named after Green Window but it seems not JR but their predecessor JNR(Japan National Railways) loved green. JNR also introduced GREEN car(1st class).
Midori no madoguchi sells nationwide tickets and able to do the seat reservation. Tickets and seat reservation tickets are sold from 1 month prior of the date of use. Which means if you are traveling on 1 July, you can buy on 1 June or later. Seat reservation can be done from 10:00, which means if you want to make a seat reservation for a train on 1 July, you can get the seat reservation at 10:00 of 1 June or later. Even if the train departs at 06:00, the reservation can be done at 10:00.
Also, JR uses 24 hours for their trains. 06:00 means 6AM, not 6PM. Of course the station staff will double check if you said "train departing around 03:00" but watch out for "train departing around 08:00". The staff will consider as 08:00 in the morning.
Then, there are very long ques during the following periods:
*Beginning of April = New school year starts around 08 April.
*27 April - 06 May = Golden Week(GW). National holidays are gathered around this term.
*11 - 20 August = Summer vacation called OBON
*28 December - 06 January
If you are especially traveling during above periods except beginning of April, please do the seat reservation as soon as possible. Then, please note not all stations are equipped with Midori no madoguchi. Smaller stations usually have 1 staff allocated and usually the staff is not so familiar with nationwide reservation. Therefore please go to the big terminal stations as like Tokyo, Ueno, Shinagawa, Shibuya, Shinjuku and Ikebukuro in Tokyo and Kyoto, Shin-Osaka, Osaka, Tennnoji, Sannomiya in Kansai area.