Guard-waypoints can be a very effective and very useful tool for mission creating, however it would be nice if you could tell the AI which guard-triggers they should protect.
In its current state, any synchronization between guard-wayoints and "guarded by"-triggers will be ignored, so when you have two or more bases on opposite ends of the island, the AI will try to walk from one end of Altis to the other.
Instead, as soon as you synchronize one or more of these triggers with a certain waypoint, the appropriate AI should only check those.