That tunnel looks a lot like what I did between my grow-out coop and the run.
My first suggestion is to come up with a way to house the chicks across wire from the older ones so they can see each other but not get to each other. That could be sectioning off a section inside the coop, putting something inside the run that protects them from the weather or something outside the run but next to it so they can get into the run. It could be on the ground, it could be elevated. Section off a portion of the run for their use, isolated from the older ones. You can use chicken wire inside the run since it is only to separate the chickens. Your biggest problem may be a way to come up with a gate or door to give yourself access. I prefer the grow-out coop as I think it gives you more control and flexibility, but inside the coop can work.
House them side by side for at least a week, I prefer more but a week might be enough. Then, when you can observe, open the door/gate between their run and the main run. Keep separate feeding/watering stations in each section. If they are in the coop, just open the pen door. That's about it. If you see problems lock them back up and try again in a week. It's fine if they continue to sleep apart for a while. I prefer they do, mine are most brutal to each other as they are settling down to sleep.
It would not hurt to put something in the run for them to hide behind, under, or on, especially if you use the separate grow-out coop. What I'd expect to see is the young to avoid the older. If they are all in the main coop, the young may be on the roosts when the older are on the coop floor. If the older are in the run, the young will likely be in the coop. Try to not force them to share a small space any more than you have to, try to give them as much space and time as you can for them to work things out.
Good luck!