I think it would be wise to separate them as soon as you can. I've seen awful pictures of baby snakes that tried to eat each other. It's probably also less stressful for them, and it seems like those first few weeks can be crucial in getting a baby snake to eat, so I'd want to stress them as little as possible! I guess it would also be good so you can see exactly when each individual baby has shed, pooped, etc. without any doubt.
I don't know the real answer since I've never bred my snakes but the above just seems like what would be best?? Babies can stay in pretty small containers for the first couple weeks, like little food containers with holes inside.