I am bit confused about Japan transportation. Is there any difference between subway and JR Railway.?

Question:

And what is the best transportation to go through Kansai area (Kobe-Osaka- Kyoto) and Tokyo.
As a foreigner, what options is the best and cheap; early buying JR Pass in my country or buy it on the spot in Japan.

Answer:

It depends - you don't say how much you are going to ride. The difference between JR and subways is that they are separate companies. You can only use a JR Pass on JR run trains, buses, and ferries. You can't use them on city subways. But most city subways have a day pass that costs about 1000 yen or so. You can't buy a full JR Pass once in Japan, but you can get regional JR Passes after you arrive, and may or may not be more economical for you. The Kansai area JR West Pass might be very
good for you. The Icoca card is essentially a prepaid card that doesn't save you much - it's only more convenient than constantly buying tickets.
So again, it depends how much time you're spending in each place, and how much you will ride the rails. If you are going by train from Kansai to Tokyo and back, plus doing a lot of travel within Kansai, a 7 day full JR Pass is probably worth it; maybe not for a 2 week pass though. Otherwise you could look at the JR Regional Pass along with a Tokyo subway day pass. There are also air passes you can get that might make it more affordable for you; take a look at
http://www.jal.co.jp/yokosojapan/
http://www.staralliance.com/en/fares/reg…
http://www.ana.co.jp/wws/us/e/wws_common…

You don't give enough info on your travel plans to give a definitive answer; but you have enough info to find what is best for you.