There are sooo many trains in the Tokyo Metropolitan area! It is a maze for people who live here; for a visitor, it may seem a huge mess. But getting around by train is often the best way to get around, so start your train-ing early in your visit.
I recommend two things to make train riding easier. First, get a Suica or Pasmo card from either JR or the private railways. You can purchase one at a machine, but it is easier to walk into a station counter and ask for help. You must buy a card for at least 2000 yen, which includes a 500 yen deposit for the card. With the card, you can get on any train (or bus) and not have to figure out the fare for each ride. You just have to remember to charge up your card, or you'll be embarrassed when the wicket closes on you.
The second thing is to ask for directions to where you are going at the station. The station attendants are very helpful. Have a map with you, which lists both the JR and other trains. There are many train companies, so a transit map that includes both types is critical. If you can, have the station or place you want to go written down, in Japanese, if possible. Then, even a station attendant who has poor English can show you the best way to get there on the map.