You have them in thier own cage inside the coop. After about a week or two of that I crack open the cage door and put a brick in the door and bunge cord the door so it wont swing open. The crack is big enough for the little ones to go out on their own and run back inside if they are getting picked on and to eat their own food and water.
My youngest got put in the juvie cage inside the coop at 8 weeks, opened the door a crack at 10 weeks and they are now hanging and sleeping with the big girls at 12 weeks old. I kept their cage in there for a while, but they didn't get picked on and didn't go into the cage so it got removed.
Another thing you can do is put a sheet of plywood up on some hollow tile bricks so it is 6-8" off the ground. The little ones can run under it and hide if they are getting picked on but the big ones can't follow and continue tormenting them....atleast untill the poke their head out for fresh again again. I had one hen that would sit on top the board and just wait for one to try and come out. She was a mean grumpy old girl who didn't like anyone or anything. In her 3 or 4 years in my coop I don't think I ever carried her or had her eat out of my hand...glad she is history.
Good luck, they will sort it out.
Cory