Regarding transports: As previously stated, you can scrap a transport ship and get back your legions. I'll leave the strategy for how many to load up to others, but there is no way (other than scrapping the ship) to take legions off a transport ship. However, if there is only 1 troop on a transport ship in orbit, when you eject said ship from orbit, you can fill it. I find this to be a bug, IMO a transport should be more malleable with respect to the troops it carries. So a transport with 2+ troops is stuck with those troops only, but a transport with 1 troop can be refilled upon leaving orbit (if you have the legions), with current rules.