My brooder is in the coop so the brooder-raised chicks grow up with the flock. I often turn them loose to roam with the flock at 5 weeks. My broody hens raise their chicks with the flock from Day 1 and wean them anywhere form 3 weeks of age to 10 weeks. I do have a lot more room in the coop and outside than you do. I have a main coop, a grow-out coop, and a shelter where they can sleep safely. Between the incubator and broody hens I may have 4 or 5 different-aged broods a year.
However they are raised, my juveniles do not merge much with the adults either outside or inside until they mature enough to join the pecking order. With my pullets that's usually when they start to lay. Who knows when cockerels reach that point. When they are outside they form sub-flocks with the juveniles avoiding the older birds. Different aged broods generally avoid each other too. Inside at night the juveniles are not allowed on the main roosts with the adults until they reach maturity. That explains them sleeping in the nests.
My definition of a successful integration is that no one gets hurt. Sounds like you are doing OK from that aspect. While they are integrating I don't care where my juveniles sleep as long as it is not in the nests and is somewhere predator safe. I used to have a problem with them sleeping in the nests so I put up a juvenile roost, lower than the main roosts, higher than the nests, and horizontally separated by a few feet to give them a safe place to go. On the rare occasions I find one sleeping in a nest I just toss it out on the coop floor after dark, just trying to teach it the nests are not a safe place to sleep, but I don't try to cuddle my chickens. Especially if they are used to sleeping in the nests it could help to place them on a roost instead.
I don't know where your older ones sleep. If they all sleep on those two roosts on the end that flat board may work a a juvenile roost. If they are more spread out you may try raising those two a bit to entice the adults to sleep there. Or lower that flat board a bit.
I'll include a photo of my juvenile roost. The top of my nests are droppings boards, horrible design as they are hard to scrape. The brooder is off to the right with the main roosts above the brooder.
That second coop gives you another option. I like that extra flexibility a second coop gives you. If moving them to the one coop causes problems let the young ones sleep in that other coop until they mature more. Let them roam together during the day but just sleep separately. I've had some move into the main coop on their own but usually I have to move them myself. I know it is a pain to maintain that second coop, may be why you want to move them, but it gives you an option.
Good luck with it.
