Within the greater San Juan area, I think you'll find no shortage of timetables, etc. It was very convenient and felt very safe to take the bus from our hotel into Old San Juan (and back).

Outside this area, my understanding (which must be derived from guidebooks, because we rented a car) is that there are designated meeting points, but the buses are privately operated. They leave when they fill up with enough people to make the trip worth the driver's while.

Jon