Before we took down the fence, Josh made a cut out to put in the doorway of the small coop which the babies could fit through one at a time but the adults would be too big for. This allows the smaller birds to escape if they are getting pecked by the bigger ones.
Then we took down the fence and crosses our fingers. Initially a few brave souls came out and got chased all over the place by the older birds. Most of the first day the youngins hid out in their coop. The next morning when I came out the big birds were still locked up so the little ladies were milling about, exploring the run in safety. When I let the older birds out most of the little ones went inside but not all - progress.
We are now in our second full day and the little birds are coming out more and more. I read an article this morning on pecking in birds, which said that cannibalism can be caused by boredom. If they have a lot of things to explore though, they leave each other be. They suggested making your run three dimensional by going the birds lots of things to perch on, scratch under, and explore.
I took some tree stumps from the wood pile in varying heights and put them in the run. I also made a little ladder of sorts where they hop up onto a perch then can pick food from a suet feeder.
They were intrigued by this and kept trying the strain their necks up to peck the food from the ground. I'm hoping that giving them more to do will distract them some from the fact that there are new creatures integrating into the flock and help the process along...