There is only one route.It takes you up to the forts and back with a little tour in OSJ.You get the trolley to the left of pier[as you come off the pier]walk down to the first street im not sure of the name and you will see the trolley.
The trolley is free and is the first street to the left of the cruise pier. Right there on the corner is the trolley sign. We took it up the hill and got off and walked over to San Cristobal fort. It circles pretty regularly. Yes, you can get on and off at different places.