A short answer because, well, time is short, but it'll point you in the right direction.
Firstly, use switch triggers to control waypoints. Search the forum, in years gone by this has been explained many times.
Secondly, NEVER use player waypoints. Players in Veteran mode can't see them. The mission always gets screwed up. If you play in Cadet mode, don't. Veteran mode is MUCH more fun. Really. It is. It takes a little bit of getting used to if you haven't it before but believe me it's worth it. Nobody who switches to Vet ever switches back.
Use variables to control your mission. Stuff like
objective2=true; objective3=false; objCount=2
? objCount > 2: endMiss=true