Can I use the JR in Tokyo?

Hello everyone.
My partner and I will be visiting tokyo for two weeks in November.
I am wondering if the JR rail will be of any use to us.
What is the difference between JR lines and subway?
For the JR pass can I use everything that has JR at the beginning of it? IE are the JR easy to see?

My journey will be tokyo center, shinjuku, shibuya, yoyogi, ikebukura, akihabara, Mt fuji, ginza, rappongi, asukusa, ueno, tokyo tower, Kamakura.

Please please help me. I want to save as much as possible :D

Will the JR get us to most of these?

My partner and I will be visiting tokyo for two weeks in November.

Which two weeks? ie. what date do you arrive?

I am wondering if the JR rail will be of any use to us.

Yes JR Rail lines in Tokyo are often very useful. The main Yamanote loop line is used pretty often by tourists

What is the difference between JR lines and subway?

The subways are owned by different companies. In general the JR lines are "above ground" and the subways are below.

For the JR pass can I use everything that has JR at the beginning of it? IE are the JR easy to see?

Yes you can, but I think the JR pass would be way too expensive considering your list below. Yes the JR lines/stations are clearly marked.

My journey will be tokyo center, shinjuku, shibuya, yoyogi, ikebukura, akihabara, Mt fuji, ginza, rappongi, asukusa, ueno, tokyo tower, Kamakura.

Where are you staying in Tokyo? Most of these places can be accessed using JR lines, although sometimes a non-JR line is better/easier or the only one available.

Tokyo station, Shibuya, Harajuku (for yoyogi park), Ikebukuro, Akihabara, and Ueno are all on the JR Yamanote line.

Asakusa, Roppongi are best accessed via the subways.

For Tokyo Tower you have a few options:-
http://www.japan-guide.com/e/e3009.html#jump_access

Please please help me. I want to save as much as possible :D

Where do you land and depart? What exact dates? Where are you staying in Tokyo?

In general you will be best off getting the Suica + NEX package at Narita. Use the NEX (Narita Express) ticket to get to and from the Narita Airport to Tokyo, and then use the Suica (prepaid card). Suica can be used on either JR or non-JR lines (subways). This will be the most cost efficient for your itinerary.
http://www.japan-guide.com/e/e2359_002.html

For Hakone consider the Hakone Free Pass from Shinjuku
http://www.japan-guide.com/e/e2358_008.html

For Kamakura there are a number of options too:-
http://www.japan-guide.com/e/e2166.html#jump_orientation

Do NOT buy a JR Pass unless you plan on making a longer trip to somewhere like Kyoto or beyond.

You can use hyperdia to look up prices and timetables
http://www.hyperdia.com/

Enjoy your trip!

Exept 4 rOppongi, and tokyo tower,
JR runs on all your distination.

You can reach ROppongi from Shibuya by city-bus or by metro-subway.

Thank you so much for your replies.
You have really helped us alot.

I am arriving at Natita on 3rd November 2:20pm (Japan time)

I think I will just get the prepaid pass :)

Thank-you so much for your help! :D

I was so confused about the lines :S

Lisa. x

If you visit Mt.Fuji, Nikko and Kamakura the new JR Kanto Area Pass could be a good solution. It allows unlimited use and reservation on JREast trains.
All infos here:
http://www.japan-guide.com/e/e2361_06.html