If you are traveling from Monterey to San Francisco on the Coast Starlight you would hand the thruway bus driver your ID card to be given to the agent at Salinas at which point you would pay for your ticket. If you take the Amtrak California Bus which is actually MST transit route 55 to San Jose I believe you would pay cash in the farebox and then amtrak would deduct that from the rest of your rail fare however with that route you would be changing to CalTrain into San Francisco so the whole trip would be non amtrak and you would just buy a separate caltrain ticket. But anytime your travel begins on an amtrak bus you simpy hand over your license or ID Card to the driver and we give it to the station agent who then sells you your ticket.
Mark
Mark