I've download official command references from the eidtors depot
Unfortuntely that is not going to be much of help as it only contains the original OFP-OFP:Resistance commands, there's hundreds more in Arma2 so your best bet is to use the COMREF here
I was wondering if theres a script command to set the On Activation of a waypoint as well as the Condition of a waypoint, via scripts.
I thought there was but couldn't find just now so maybe there aren't (which is weird because for everything else there is).
Anyway, using waypoints to control events in a missions is very bad design because waypoints may never get activated for some reason or another (this info is directly from the game devs btw so not something I cooked up
Other problem is that in A2 the AI choppers are extremely picky where they want to land so they may never land even near where you want them to, and they prefer to land on the 'helipads'.
Anyway, this can be done without any waypoint scripting involved, how it's done exactly depends on whether the destination trigger is created dynamically or pre-set triggers are selected randomly. And does the trigger do something specific or is it just a position.