Some pecking is normal as they sort things out. As long as no one is bleeding or being injured, I would just let it play out.
As far as putting the little one's in, my philosophy is to ingrate them as early as possible as I've found that most older chickens generally pay little mind to younger chicks, and it actually becomes harder to ingrate if you wait too long.
My approach is as follows. Once the chicks are around 3 weeks old, I section off an area of the coop for them. I'll put a mother hen brooding pad in there if they still need heat. When they are 4 or 5 weeks old, I open up a chick sized passage way to the main coop, so the chicks can go explore the coop, but have a place to safely retreat to that the big chickens can't get to. By 6 weeks old, I remove the partition. There is still going to be a little pecking and chasing, as some of the older chickens make sure the youngsters know their place, but nothing out of the norm.