Hi Shrader,
We are using our dog cage and run to separate Mama and the chicks from the rest of the flock. For the first week, we just used the dog cage in the hen house. We put cardboard on top in case another hen jumped up there.
Earlier this week, my husband set up the dog cage so the opening lined up with the small door into the run. So we open the ramp each day and Mama and the chicks have access to the run. The other hens can't get into the run for now. We leave the big door of the hen house open so they can get out. Now that the weather is getting warmer this works ok, but I'm not sure what we will do if we get a cold snap, or a rainy day (which is predicted tomorrow). The hen house may get wet if we leave the big door open in the rain.
When we are home, we've opened the run door and let Mama and the chicks mix with the rest of the flock. Sometimes one of the other hens gets curious, but Mama chases her off. The chicks stay very close to Mama.
This is working for now. It's been a lot of trial and error for us. We didn't think things through ahead of time and prepare. If Mama gets broody again next spring (which I hope she does), we think we may build a wooden brood box in a corner of the hen house and we've talked about possibly building a smaller run on the other side of the hen house. This may be a good idea in case we ever have to separate hens anyway.
Good luck Shrader. It is fascinating to watch the mother hen's dedication to the eggs and the chicks once they are hatched. It's been a great experience. When I get home I'll try to take some pictures.