yes you can. like has been said, the only thing you have to remember is that the transport has to be deployed when its "parent unit" is deployed.
i often use a farseer, who can purchase a serpent, but deploy the serpent in one place, and the farseer in another vehicle, either a falcon, or in anotehr serpent joined to another unit. the seers serpent is empty, but provides a useful distraction and mobile gun platform... perfectly legal, plus, the seer is still hidden! can cause a great amount of confusion for the enemy, and keeps them guessing as to my tactics!