I have a pretty good sized coop with a large run, which opens to up free range when I deem it safe. When I put youngsters in the coop, I have an area under the community laying box that only the small ones can run under. I have the food and water next to the box. They learn pretty quickly to run under their safe haven spot. When the herd goes out into the main run, or to free range, the smaller ones come out and eat and drink and get the feel for the coop. When they get scared, they run under cover. Within a few days, they are running out with the flock, but can still get under cover for another month or so if need be. Ive not had a problem with this system, they all end up getting along.
That being said, I have mostly rocks and marans, which are pretty mellow girls.