JR Yamanote Line

I am using JR east-south Hokkaido Shinkanshen from Hakodate and arrives in Tokyo Station, I need to transfer to Shin-Okubo area. Once I arrive at tokyo station, how to transfer to JR Yamanote line, which track / floor i need to go.

Just follow the signs in the station.

You have two ways of going to Shin-Okubo station from Tokyo station, using JR.

1. Take a Chuo Line rapid train at the track 1 or the track 2 (both are for the same direction, because Tokyo station is the terminal of Chuo Line), and change at Shinjuku station (the 4th stop) for a Yamanote Line train (direction of Ikebukuro station, i.e. the outer ciucular line, at the track 15). Just the first stop. Less time.

2. Take a Yamanote Line train at the track 4 (direction of Ueno/Ikebukuro, i.e. the inner circular line). More time (32 minutes) than the way 1.�@

I recommend the way 2.

Once i arrive tokyo station from Hakodate by Shinkanshen bullet train, which floor/track i will be arrive, if i need to go to JR�@Yamanote Line, do I need to change floor/track inside Tokyo station, ie is all at the same floor ?
Do I need to exit the gate & re-enter ?

It may sound and look complicated but Tokyo station is well organized. Just follow the signs.

And yes, you will need to get out of the Shinkansen part of the station into the "normal " JR part of the station and go to the Yamanote line tracks. Just allow yourself some time to orient yourself.

On the internet you might also be able to find detailed maps of Tokyo station, but they can potentially only confuse you more.

Enjoy your trip to Japan!

Maps are readily available on the JR East website.

As soon as you get off the shinkansen, you will see signs overhead pointing you to the gates that will be closest to different train lines. The Yamanote line is a bright green color, very noticeable, and will also be labeled in English. You do need to go through the shinkansen gates into the general JR ticketed area but it will not be hard to find. If you would really like to know the platform number, it is #4, bound for Ueno. (The Yamanote trains leaving on platform 5 are going in the opposite direction on the loop.) Don't stress yourself too much!

You can see a map here, but it makes the station look much more complicated than it really is.

http://www.jreast.co.jp/e/stations/e1039.html

If you have any problems you can ask the staff there. They will help you go from the shinkansen area to the regular JR area.

Transfer at Ueno.

As others have said it is quite straightforward but if it worries you then @Firas has the answer, change at Ueno. That's what I would do.

Concerning station structure maps, I know opinions are divided, but I also understand one wants to be prepared in advance, although one knows signs might be well prepared.
JR station maps surely look confusing at a first glance, but not so confusing when you know how they are designed.
So, take a glance at this map, and study it.
http://www.jreast.co.jp/e/stations/e1039.html.
You have the enlarged version in PDF.

There is also HAYABUSA which skipped Ueno, just not all.

Transfering at Omiya is the fastest, all HAYABUSA stops.
http://www.hyperdia.com/en/cgi/en/search.html?dep_node=SHIN-HAKODATE-H...
https://goo.gl/maps/qz4SosmWbhT2
(Change dep date and time)

Omiya :
http://www.jreast.co.jp/e/stations/e350.html
Ikebukuro :
http://www.jreast.co.jp/e/stations/e108.html

Also you can back fr Shinjuku by Rapid train until Shinjuku first, some mins faster than transfering at Ikebukuro.
Shin-Okubo is not a Rapid train(as Shonan-Shinjuku line) stopping station.
http://www.jreast.co.jp/e/info/map_a4ol.pdf
http://i.imgur.com/d8cO4Eu.jpg
Shinjuku :
http://www.jreast.co.jp/e/stations/e866.html

There is also HAYABUSA which skipped Ueno, just not all.

Currently there is only one Hayabusa that skips Ueno on the way from Shin-Hakodate-Hokuto to Tokyo (the number 34). If OP is unlucky enough to ride it, adapt accordingly.