Dealing with rats is a tough situation. A few years ago, I faced an infestation where the rats had tunneled between two runs. It was like playing Whack-A-Mole. I would think I had dealt with them in one place, only to have them pop up in another.
I revamped the runs where the tunnels were, added hardware cloth to the two attached coops that had dirt floors, moved the feeding station for the ducks far away from the chicken coops, added essential-oil drenched cotton balls to the tunnels and refilled them -- and still, rats.
I am staunchly opposed to killing wildlife. But, I finally exhausted all the non-lethal methods, and the best way to get rid of the rats, for me, was an electronic trap that zapped them. I didn't have to even touch the rats -- which I honestly felt sorry for. All they were trying to do was survive in this world.
However, I also needed my birds to survive and once they crossed into the coops, I had to do something.
As far as integrating your flocks, I have to admit that I am Very Bad at that -- which explains why my property looks like a trailer park for poultry. I have LOTS of small coops with two to five chickens in each (The seven ducks and the two geese each also have their own spaces).
Welcome to BYC -- hope you get the rats under control, your build completed and your flocks integrated, if that's what you choose to do!