To answer the second question first, it's a difficult problem. One solution - which isn't always very practical - is to have a friendly dude hop into the empty vehicle at the start of the mission, then deleteVehicle him. This makes the vehicle appear more friendly to your group leader. The problem is of course that the enemy start zapping it.
Alternatively reduce the number of LAW soldiers around to do the attacking.
Your difficulty with sorting out trucks is completely solvable however. Give the truck a move waypoint where you want it to wait: in the condition field of the waypoint write
truckMove
Now create two triggers over the area where the dudes are going to be. Go into groups mode (F2) and group one trigger to each group..... that isn't very clear so I'll say it again. You have two triggers: one is grouped with group Alpha and the other is grouped with group Bravo. (Drag and drop a pale blue line from the trigger to the group leader.) The trigger will detect if the group is present - you get special options in the activation box, just play around with it till you get what you want.
Now, in the "on activation" field of each trigger write
truckMove=true
What all this means is that the truck will wait at the waypoint until the variable truckMove becomes true. TruckMove will be set true when either group enters the pickup area.
Hope that does the trick