When you hear the name of your stop announced, press the "stop" button. If you Japanese language skills are limited, the best bet is to sit at the front of the bus (on the left) and tell the driver your destination - they are a friendly bunch and will let you know when you have arrived.
To pay for your fare, place the ticket and exact change into the machine to the driver's left. If you do not have exact change, please note that there will be a machine providing change (up to 1000 yen notes). It's best to change your money before you reach your destination, so as to not inconvenience other passengers. If you are using a route on a regular basis, it is possible to buy discount tickets and pre-paid cards at the major stations.