Seperate them now. If you seperate them fom the start you give each one the best chance to grow up strong without any beginnings of co-habitation stress.
Notes about critter carriers:
1) The tops: There are two reasons why you should consider replacing the tops. The first is that they filter out so much of the light you need to get into the cage for the chameleons. The second is that taking the top off (and back on)rocks the whole cage and is both visually and vibrationally (is that a word?) a major event to the little baby chameleon. That is a lot of stress for the baby wondering if the earthquake and thunder is just a prelude to being eaten by the horrible creature that is peering into his cage. An alternative is to use a large rubber band (office supply store) and fiberglass screening (home improvement store)to create a top that will allow light through and can be silently taken off. True, visually, the chameleon watches his whole sky being removed everytime you have to clean and feed, but do it slowly and quietly and the chameleon will have the elast bit of stress as possible in this situation.
2) The walls: You run into the classic problems of aquariums. A screen top helps out a lot, but make sure you keep the cages very clean! Outside the walls it would be best to place visual barriers between cages so they don't see each other. Chameleons seem to quickly adjust to the sight of others if they know their territory and they know their territory is never invaded by another, but it is simplicity in itself to put up a piece of cardboard or something so the babies can't see each other.
3) The floor: Be very careful about water gathering on the floors. You would be amazed at what little water a chameleon can drown itself in. If there is any gathering of water you run a risk. Chances are, if the chameleons are happy, they will stay in the branches and this won't be a problem, but don't count on it!
Whew!
Bill Strand