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.

A potential area where people would get confused is with the Chuō West line where the Nagoya to Nakatsugawa section is in the JR Central IC card area, but not further north. Or from the northern end at Shiojiri where itself is in the JR East Capital region IC card area where visitors are less familiar with the different ways.

Any route that passes through Atami station on the Tokaido line is another one: you can use IC cards to get to it, but not across to the other side. While you can get out of it if coming from a JR Central’s IC card zone you cannot get in with it and would need a paper ticket. The ones you see are for JR East Capital region, but you can use these with the paper ticket to get in.