First you need to know there are Trains (overground), Subway/Metro (underground), Monorail, Trams (e.g. Hiroshima). A station could have a multiple services. You will need to transfer between lines. Stops are everywhere, great coverage. Different lines owned by different companies, so going to A from B likeily need to do a transfer between lines that you will need to buy two tickets.
That's why a prepaid e-money card like Suica (You can order overseas before you visit Japan)2, ICOCA or Pasmo is awesome. It saves you enormous amount of time because it works on paying for all lines. You can't use Suica for Shinkansen1. You can also use the e-money card in convenience store, supermarket, some restaurants, and coin lockers.
- Google Maps
- Apple Maps
- JR app