I have two coops attached to the same run (a top coop and a bottom coop). We put the 5 week chicks in the bottom and the first few day we had the entrance completely blocked off. Then a couple of days ago, I opened it to the run, but with a small enough opening that the big hens cannot get in (though the 10 week old chick has decided she is one of them and squeezed in and hangs out with them. She is super nice to them and cuddles with them. She looks funny in there because she is twice their size and they are blue EE and she is a barred rock lol). The chicks go out occationally and run into the coop if the big ones come close.
I plan on doing that with the 3 week old chicks when they can be without a light. The have two heat lamps on them in a brooder in the shed. If it warms up a little more, I will go down to one and then eventually one at night and then take it off.