Ask the Driver
I've lived in Japan for about 4 years, and I'm still very confused about the bus system, mostly because all of the stops listed between the starting and ending point are very small neighborhood areas with names that you really won't know unless you are a regular rider, or you live in the area.
The bus drivers will of course know the route by heart, so if you are trying to go to a specific location such as a museum or restaurant, you should confirm with the bus driver as you get on the bus. Be sure to say the name of the place you are trying to go very clearly if you don't speak Japanese.
Bus drivers are much less likely to speak English than say cab drivers or train station attendants. But don't be afraid to get on that bus and see some tucked away corners of Tokyo!