There are so many ways to go to your destination by train, especially in Tokyo. One handy website to help you get to your destination is Hyperdia which is in Japanese, English and Chinese.
At “Timetable and Route Search,” located on the website’s top left, choose your language and then search how to get your destination by date, time, departure or arrival.
Hyperdia is ideal if you’re not sure how to get to your destination.
Also you can get Hyperdia Application at iTune store.