Sounds like the roo will have to figure it out quickly, how old is the roo? We had chicks integrate with their papa with no issues. The roo was just over a year and had by the alpha from day one had been with the hens from day one. Not sure that helps. We had our chicks I. Our covered run while they grew out, while the flock free ranged during the day. The chicks had their own coop to start, then around 6 weeks, when they were big enough to free range without being a chicken nugget for a predator, we let them mingle and blocked smaller coop. We had not issues like I said, need to allow the flock to have visuals on the babies at firs, just like integrating a new bird to the flock.
Thanks for the input! He's only 4 months, so I'm hoping that's most of the issue, and he will just naturally move to alpha as he fills out and matures. Depending on how things go I might have to adjust my plan with the chicks. i was planning on setting up the brooder in the coop, just section off a part of it, then setup a "safe zone" after a few weeks where the chicks can wander into the coop with the big hens if they'd like, but can escape back into the brooder through several chick sized openings. I'm hoping to integrate them as soon as possible...but I also don't want anyone getting too beat up... It's all a great experiment for me still, so any input is valued. I love hearing how others set up their coops/runs/pastures!