I must admit that the moment I landed in Japan I had a friend that helped me figured out which train to take and how to get home. If you will be traveling a lot, I am certain that you will be able to figure out the map pretty quickly but if not have no fears, Google Map is an amazing tool to have. However, this might be very surprising for some of you who are reading this but many of us ( including myself) assumed that Japan would have wifi everyone, IT DOES NOT.JAPAN DOES NOT HAVE WIFI EVERYWHERE OR ANYWHERE FOR THAT MATTER. Therefore I usually google map the direction, screen capture or write it down before I leave the house and I recommend you do the same unless you are pretty fluent in Japanese than that's an exception :D .
JR Line Above vs. Underground
Here is a complete, detailed map of the JR line ( this is different from the JR metro aka subway line ) JR MAP. In the beginning, I used this a lot more than the subway, later on when I became familiar with the environment I started using the metro more simply because it gets me to exactly where I need to be. You might be wondering well if it gets me where I need to be why don't i use it ? I must admit that I was used to taking the Yamanote line and the walking a bit extra because I was more familiar with the path than to take the metro and then get lost because personally I think it was a bit more complicated ( they don't have screen inside the train to tell you where you're heading in both English & Japanese )
Understanding the Map & Tickets & Transferring
The link the the map as well as the one below has many different colors and that is because each line ( yamanote line, chuo line and etc. line has a color for their own ) The one you will be using the most would be Chuo Line which is Orange. Here is another map if you want to take a closer look Simple Map. Yamanote line as you can see from below is green. It stops by major places such as Tokyo station, Shibuya, Shinjuku, Ueno and etc.
There is usually an English version of these map but if not than I usually write down the character and ask the person next the ticket gate. But overtime you'll get used to what the character looks like and you won't have to ask for help anymore. Next the each location is the price to get from wherever you are at to that location. This is very useful when you decide to buy ticket because you forgot your Pasmo/Suica card at home. On the vending machine there is English so it shouldn't be too difficult to select where you want to go and then just insert that much amount of money then it will spit out a ticket. After you entered the gate for the first time the give you the ticket back, hang on to it because you will need it to exit the station later. If you are transferring you will stay within the station, so continue to hang on to the ticket. Once you are at the destination that you indicated when you purchased the ticket, it will keep that ticket and you can just exist.
Rush Hour & Late Night Outing
It can be very hectic at the station especially at Shinjuku because all of the major lines meet up there. The place is especially crowded around 8-10pm because that's when people get out of work or go out at night. Most train stopped at midnight and starts again at 5am. If you happened to be stranded some where taking a cab is really expensive to come back home so make sure you keep track of time. However, I have heard that people spent the night singing karaoke and rest there until morning.
At the Platform
If you have made it to the platform congratulations ! As you can see in this picture there are many different lines and they are indicated on the ground if you get a chance to take a look, simply because it has been marked to match with where the doors for the train will open. One of the things to keep in mind is you should definitely let the people exit the train before coming in and if you're on the train and people cannot exit, step out to let the people leave and then you can come back in. There's always at time board at these platform informing you when the next train will arrive, where it was from and where it is heading to both in Japanese and English ( similar to the one
In the train
Once you're in the train keep in mind that it is a public space so don't speak to loud or blast your music even though some other passengers in the car might be. One of the thing you will definitely refrain from doing is talking on the phone in the train, I have received glares before but my friend was leaving Japan and I wanted to say goodbye to her. Other than that if you're interested in looking the road while you're in the train as well as seeing the work of the driver don't be afraid to go to the first section of the train, it's a lot of fun !