My brooder goes in a sectioned off area of my coop. I have tall sides and put a wire screen across the top, when they get big enough to jump out.
I can't help with pest control. Since the area I started my flock in never had chickens around, I've never had any pests problems. I've heard they can be brought in by wild birds, but it hasn't happened here. I've also never brought in any adult chickens. Only hatchery chicks and my own hatches.
I once worked on a ranch in S. W. in New Mexico. There was an old chicken coop, that had not been used for several years. The owners bought some chicks and started a new flock. The chickens became infested, with the soft body red chicken ticks. The only thing we could come up with, was that the ticks were able to "hibernate" in the thick adobe walls, until the new chickens were brought in.
We relocated the chickens, dusted them with seven and sprayed the coop with I believe malathion, to get it into the dirt walls. Not exactly organic, but it killed the ticks.