It's not so. More mature birds outrank less mature birds in the pecking order and are likely to peck the younger if they invade their personal space. It usually doesn't take that long for the younger to learn to avoid the adults. My pullets typically stay separated until they start to lay. That seems to trigger the adults seeing them as adults, not immature brats.
This separation before maturity is day and night. Mine typically avoid the older ones during the daytime and will not sleep on the main roosts with the adults at night. The problem is when they are going to sleep. If the pullets fly up to the roosts while they can still see the older ones will probably peck them unless they are pretty far away. With you only having 6 birds and that small of a run it's likely your coop is pretty small. When you are integrating that 4 square feet in the coop and 10 square feet in the run don't mean anything, especially if there is a maturity difference. They need enough room to run away and get away and enough room to avoid in the first place. If your three older ones are in the middle of that run the young ones can't get that far away. It's pretty typical for the juveniles to be in the coop while the adults are in the run with that kind of set-up. That's a good way for them to avoid the adults.
All this changes when the juveniles mature enough to be accepted by the adults. They may still hang more with their buddies they were raised with but they can sleep next to each other and eat next to each other without a lot of drama. Usually the transition from juvenile to sleeping next to the adults comes with very little drama. I usually don't notice it happening until I notice it has already happened.
It's not always as bad as I made it sound. Each year my flock has a different dynamic. Some years even young chicks mingle a lot more than others. Chicks raised by a broody hen with the flock often have it easier, though often doesn't mean always.
It sounds like yours are doing OK in the run during the day, even in that small run. You are doing pretty good there. It's them sleeping together that's the problem. To me, that implies that your main coop is pretty small. The juveniles can't find a place to sleep in there where they are safe from the bigs. You can try what you are doing about swapping sleeping places. Sometimes stuff like that does work. But you may need to let them sleep separately until the littles move into the main coop on their own (that does sometimes happen). Or try moving them in when the juveniles start to lay.
It is far from hopeless but integrating in small spaces is harder than having a lot of room. Good luck!
