Questions:
- Is the player supposed to be taking part in the ambush?
- Are other Starfleet NPCs taking part in the ambush?
- Are we talking space or ground map?
- If ground: Does the player see the convoy all the time (e.g. are there any walls/rooms)?
Suggestions/Hints:
Currently we have no way of actively setting waypoints, so it is not possible for an NPC group to go to a specific place. You can enable "wander" ("Behavior" tab), however the movement is rather random and it doesn't work on space maps.
There is also no way for NPC groups to trigger anything. You can't make the Starfleet group ambush the convoy, when the convoy reaches a certain point. You can only make Starfleet ambush the Klingons when the player (your character) reaches a certain point. All triggers in the Foundry need to be triggered by the player!
There's only one small workaround where you can make the player wait for another trigger to start, by letting NPC groups kill each other in a sealed off part of the map. But I have the feeling that's not really what you are looking for.
What you could consider is having the Klingon/Starfleet NPCs appear (=beam in) once the player reaches a certain point on the map. In all likelihood you have to rewrite that part of your mission.
I hope I could help you a bit.

Maybe other authors have suggestions as well!
In general I would suggest you try to make some non-mission maps to get a bit of a feeling for the Foundry tools. They are limited, and a bit awkward at times - but once you get a hang of it, you can achieve quite a lot. It's just that sometimes your story has to accommodate the Foundry's limits.
Links to Tutorials/Guides:
I would also suggest the following links for some tutorials and guides:
-
STOWiki Foundry Guide
-
Foundry 101 Tutorials