If I were in your shoes, I use three radio command (0-0-1, 0-0-2, 0-0-3). If the player are in the ground near to pick up zone, he/she can use the radio command. And when the radio command is activated, the correct squad start to embark into the BH. And when the BH is near to the drop point the squad which in cargo, start disembark...
OK. I know it's not too detaild, but I don't know how experienced are you in mission editing. Please ask detailed!