JR rail pass - reserved seats

My husband and I will have a JR pas while in Japan. We will be taking a couple of long hauls on the Shinkansen. I understand that the pass does not mean a reserved seat but I believe that in major stations like Kyoto, Tokyo, Sendai, etc. that there is a kisok/booth where you can obtain a specific seat number on a specific train. Is this correct and if so how much do they charge? Any specifics on how to find such a kisok/both?

Right. The JR Rail Pass is your ticket for all JR trains ( excluding one specific type of Shinkansen ). In addition you can reserve a specific seat on the shinkansen or the express trains without any additional fee by just going to the green window ( midori no mado guchi ) at any train station and ask for free reservation by showing your JR Rail Pass. You can do all your seat reservation in one visit or you can ask for reservation on day of travel up to some minutes prior departure. I recommend you write down what you want to have reserved, so it is easier for the Japanese railway staff to understand clearly what you want. Do not miss to read the pages on this japan-guide, too: http://www.japan-guide.com/e/e2016.html

Seat reservations are free with the Japan Rail Pass.

You can make reservations at any JR Reservation office found in most JR stations.

Reserving seats is so easy for those of us that travel to Japan regularly that we forget the simple things... althought it is called the green window, in major stations it is an office behing glass doors, in a central location (not far from the turnstiles). inside there is a counter and several staff. they do reservation but also sell all sorts of tickets, passes etc. as even Japanese travellers prefer to talk to a person than fiddle with a machine (even thought the later are easy enough to use for basic tasks like buying a single ticket). If you have used trains in Western Europe many times it will all look and feel familiar to you.

Just want to second Peter's suggestion to write down travel information prior to walking up to the reservation window. In my experience too, this makes it so much easier to do this quickly and get exactly the reservations you want. Note that you can make reservations at any JR station; you don't have to go to a shinkansen station to make reservations for the shinkansen, etc..

Just a comment.
The vast majority of signs won't say "Green Window" in English and if you were to ask people where the green window was (if you can't remember Japanese to say midori no mado guchi) if they understood english they might think you're looking for a actual green window, or just be confused.

The signs that appear in English will translate into and just normally say "Reservation/Ticket Office" on the sign, with the familiar logo of a man sitting in a chair.

If you are getting into an ordinary car (not a green car) on a train, how do you know which seats are reserved? Are there specific cars on each train that are reserved seats only and the rest of the cars are non-reserved? Or do you sit down hoping that you are not in someone's reserved seat?

specific cars are non-reserved others are reserved. On the shinkansen lines it is indicated on the platform and in the cars in English. On some minor express trains in the cars sometimes only in Japanese.

If you are getting into an ordinary car (not a green car) on a train, how do you know which seats are reserved? Are there specific cars on each train that are reserved seats only and the rest of the cars are non-reserved? Or do you sit down hoping that you are not in someone's reserved seat

There are specific cars that say RESERVED or UNRESERVED, there are signs on the platform signs, on the platform themselves, on the train car and announcments on the train itself, if you have a seat reservation ticket, your seat reservation will also indicate which car number and which seat number (ex, Car 4, seat 5 A/B/C etc).

So in most cases there shouldn't be any mistake of a person with no seat reservation sitting in a persons seat who has a reservation, as the cars are seperated.

SanSanee,
You may find very useful a weblink to 'Hyperdia' provided here in Japan-Guide. Hyperdia is a valuable english language aid in planning your trip[s] on JR lines.
You will find it in the travel header in the trains catagory.
The Hyperdia site allows you to enter your origin and destination stations and time/date and from there will show you the fastest or most direct train and schedule for the places you wish to go. When i wanted to take JR I would look up my planned schedule in Hyperdia and write down the specific train name and number etc. then at the reservation window simply present my request.
You can also use your JR Pass on many JR busses.
Have a great trip!
MP yori