let me see if i understood, you want to know how to make the vehicle wait for the troops to get in, than move to next waypoint?
Quite simple, you can create a "get in" Waypoint from the troop, than a "load" Wp from the vehicle, than synchronize them. With this, if the vehicle arrives before the unit(s) to the Wp, it will wait untill the load is done, than move to next Wp.
To make a unit get out from a vehicle:
After the load, that i explained before, crate a "transport Unload" (from the vehicle)Wp where you want the troops to get out, than, next to it, create a "get out" Wp(from the unit(s)).
You don't need always to use commands, only if you want the unit to get into a specific location of the vechile.
PS: if you want to make the chopper wait for the units on the ground, i think you can use the land command: Just put in the "In Activation" field:
Choppername land "land". I haven't tried this, but seems pretty obvious, i don't know.
Sorry for the bad English, i'm BR. Hope i could help.