Hi again!
Yes the bullet trains or as you may find them called in Japan, the Shinkansen can be used by the JR Pass.
There are some train services not covered by the JR Pass, these are called Nozomi and Mizuho trains. However you can ride the Hikari and Sakura Shinkansen instead, they travel the exact same route.
Don't worry about all the names I mention, these are just names for a certain train service and indicate how many stops a train will make.
Also with the JR Pass you can just tell the JR Staff where you wish to travel, they will then find the best route for you and there's no need to do it yourself.