The photos help a lot. I agree that maybe cardboard dividers would help on the roost when the time comes, but more likely the fact that you have 3 separate roosts should be enough to give the babies space away from the hens when the time comes.
I'd still work on run integration as more space = easier integration. I can't really tell from the photos but if you don't already have clutter in the run I'd add some to break up line of sight and give the babies places to hide. The chicks may wander into the coop to explore and that's fine, but I wouldn't keep them in there overnight yet. You want to make sure they get along fairly well outside first, so they're safe, before locking them into a smaller space at night.
I'd still work on run integration as more space = easier integration. I can't really tell from the photos but if you don't already have clutter in the run I'd add some to break up line of sight and give the babies places to hide. The chicks may wander into the coop to explore and that's fine, but I wouldn't keep them in there overnight yet. You want to make sure they get along fairly well outside first, so they're safe, before locking them into a smaller space at night.