Okay this is what I usually do,
when the battle begins I give the chocobo one of the greens, and then attack the enemies afterwards, make sure though that none of the attacks you do hits the chocobo otherwise it will attack you and then run off.
You might need one then more green though, just in case the chocobo finishes it off before you've killed all the monsters with it
Once you've killed all the monsters you would have caught yourself a chocbo