The monorail has two stops. The main one is in Tomorrowland, as it is an attraction at Disneyland. The other stop is at Downtown Disney, next to the Rainforest Cafe.
When you go up to the monorail station at Downtown Disney you will see a table, and that is where security does a bag check. Once you go through back check you give your ticket, just like at the main entrance, and go through the turnstyle. You then go to the upper level where the monorail boarding area is located.