Well say you were wanting to make Celtic Reserves Celtic's B Team, you would, I think, have to create a team called Celtic Reserves, then give them the same stats as the real celtic reserves. Then, under affliated teams, choose Celtic as parent club and select the B team type, as well as letting players move for free. You could then swap them into any division. Remember you need to move all the reserves over aswell. Then, if you play as Celtic, after 1 season, reject the offer to play in the reserves league.
There may be a simpler way to do this but this is all I can think of. Hope this helps.