Travelling by Train in Japan
Getting from A to B using the railway services is a great way to get around Japan. The country is small enough to make most journeys reasonably short and the entire setup just works. Period. Trains leave on time and they're clean, efficient and reliable. Not all trains are equal, though. The Shinkansen high-speed trains will get you between major cities with insane efficiency, but you won't see much more than tunnels and landscapes zipping by at the speed of light. But there's much more to the Japanese train network than just the bullet trains. Going to that hot spring place far out on the Japanese country side gets all the more interesting and releaxing when done using a reasonably paced train service to get there.
And Shinkansen is fantastic when you want to get from Tokyo to Fukuoka in a heartbeat. But the local, slower train services, that's where the magic happens. Getting to that hot spring place far out on the Japanese country side gets all the more interesting and relaxing when done using a reasonably paced train to get there, such as the Yufuin no Mori service run by JR Kyushu.
JR Rail Pass
If you're staying on JR lines, simply navigate yourslef to a ticket reservation counter and let them know your desired origin, destination and departure time. I sometimes come prepared with the exact sequence of train numbers if the routing is complex and I want to avoid misunderstandings, but usually it's not needed. If you want to use your rail pass, present it before telling them where you want to go.
When travelling on a non-JR line, procedures vary a bit. Keep in mind that you sometimes have to purchase two separate tickets – one for the journey itself, and one for the reserved seat. This can be pretty confusing at times and it might take a while to figure things out, but it usually works out.
Getting on the Train
The train, car number and seat number are printed on the face of the ticket. Sometimes they forget to print the english version, but you should be able to figure most things out even if you get the japanese one. If it's a paid ticket you can walk up to the automatic gates and insert the ticket, and if you're using the rail pass you will have to go through the manned gate and present it to the staff before being waved through.
The Japanese usually flood their train stations with signs and info, so it's usually incredibly easy to find out what track your train departs from and exactly where the car you're in will stop. Keep in mind that some trains have 15+ cars, so you want to position yourself along the platform before the train arrives. Many stations have lines painted on the platform indicating where the queue should be for each car and if that's the case, simply do what the locals do and line up.
Japanese trains are typically optimized to fit the maximum number of people possible, leaving little or no space for bags except for the overhead luggage racks.
Here's what I do when I'm travelling on the Shinkansen with a large or heavy bag that won't fit the overhead racks – there's a space behind the backs of the last seat row, counting from the direction of travel. If my bag has four wheels I shove it into the corner between the seat backs and the wall, and fold down the wall-mounted table next to it and boom, problem solved. The table keeps the bag in place.