clearmagazineCargo ammocrate
will make the ammocrate empty of all mags
clearweaponcargo ammocrate
will make the ammocrate empty of all weapons
I see no other way of doing it but to first remove everything and then add the stuff you want.
What comes to the Q#2, is if you want the dude in the car already when missions starts do as Macguba there kindly said, but if you want the guy to board the vehicle during mission you should use
unitname assignascargo vehiclename
unitname ordergetin true