When you choose a movement mode and then place the cursor over the vehicle you want them to board, the icon will change into a 'down' arrow. If it's yellow, the vehicle doesn't have enough room. If it's green, click it and the troops will climb in.
One thing I didn't realize until recently on this... if you have the vehicle moving toward the squad, and the squad moving toward the vehicles with a 'mount up' order, the vehicle will stop (even if it hasn't completed its movement) and let them climb in when the two meet.
The point being that even if they aren't sitting right next to each other when you give the movement order, they can still each head towards each other and mount up.