Where do the younger ones sleep at night? Can they get to it from the shared run? I'll also ask for the size of you coop and run. Some photos showing what you are working with and how they are set up could be really helpful. It sounds as if your coop may be pretty small if there is no room for a crate.
I want mine to prove to me that they can coexist in the run together with no issues before I try to put them together at night. They don't have to mingle and play together, they typically stay in separated sub-flocks, but no one is going out of their way to be a brute and a bully. I want at least a week with no drama before I try to move them into the main coop.
When I'm ready, I wait until it is dark so the chicks are easier to catch and the older ones can't see to hurt them. Then I lock them in the main coop. I don't put them on the roosts, mine aren't likely to sleep up there with the older ones anyway. I just put them on the coop floor, they'll figure out where they want to sleep. I don't care where they sleep as long as it is predator safe and not in my nests.
Then, as Aart said, I'm down there when they wake up to see how it is going every morning until I'm sure it isn't going to be a disaster. With mine that's never been more than two mornings but I have a nice 8' x 12' coop. The young ones have room to get out of the way. It's pretty common to see the younger on my 5' roosts while the older ones are roaming the coop floor. They are up there staying out of the way.
Mine can get to their temporary sleeping spot from the run. When I move them into the main coop I lock that up where they cannot get back to it. Most of the time once I move them they put themselves to bed in the main coop, but occasionally I have to lock them in there for a few nights before they all get the message. If your coop is so small they can't get in without getting pecked they might not want to go in.
I keep talking about the size of the coop. Size is important. If your main coop is big enough this should not be that hard. If it is small this could be challenging.
Good luck!