1. Use switch triggers to switch the loon from a move or hold waypoint setbehaviour "safe" to a s&d or guard waypoint with behaviour aware or combat. The trigger is fired by east detected by west, or east present, or whatever you like.
If an enemy loon walked past and your loon did nothing about it, he either didn't see him or was set to behaviour careless. It's nothing to do with the waypoint.
You can place a waypoint right on top of a unit in the Editor. To edit the unit afterwards press the shift key.
2. If you're talking about AI loons, say in a cutscene, it's easy - just set up waypoints and the odd line of code to make them do what you want. Dynamic ones that work in a mission are more difficult. There was a thread about this a few weeks ago, use the forum search function.