We added 12 two month olds into our flock of 12 hens and one rooster. We (I) was not ready but we had to do it because of a breech in security in the little coop they were in. The hens pecked at the babies....lots of running at them. THEN the rooster stepped up. He would place himself between the hens and the little ones....run the hens off if he needed to. Then he would turn and show the babies little treats. He even stations himself now between the two. I am so darn proud of my rooster. The hens accepted the little ones and they went right into the coop at night to sleep on the lower roosts. Now, I have 25 more from the second hatch that have got to build a new coop and run for and am running out of time!!
It can happen. They can intergrate. Sometimes it is a little ugly.
However, if they have been in there a few days already the pecking order is most likely established for now.