I know this is a bit older of a post but I wanted to clarify something since as a former FS boat captain, this confused a lot of people.
These routes are not fixed. The routes described above are the 'ideal' routes but often early in the morning and possibly every now and then throughout the day, they will only run one boat in the lagoon. When this happens, the route is Mexico-Morocco-Germany-Mexico. There is never any notice given since the captains have no advanced warning. When you go to get on the boat, just glance and see if there is one or two boats in the lagoon and if you only see one, ASK! Also, keep in mind that even if the boat runs between Morocco and Germany in the morning when you first get to Epcot, there is a very good chance that it will not be the next time you go to get on.