How to use the ワンマン (one man operated) train in Japan at unmanned stations that don’t use IC cards:

Hokkaido: board and alight at the front door.
Elsewhere in Japan: Board at the rearmost door of the front car, and alight from the very front door.

In both cases, you take a numbered ticket as you board, just like with buses. Other doors, including those of other cars, would not open except at manned stations. If you have a valid pass or ticket (a green-coloured ticket bought in advance elsewhere) you don’t need the numbered ticket, but do need to show it as you alight.

Some of these lines have stations inside an IC card region, or straddle between different ones. You can use them only between stations of the same zone. Not to outside of it or of a different zone.