How many chickens each, and how large a building?
I can envision something with a center isle and two coop areas at each side that you can access from the inside for cleaning and maintenance, each could have their own run area outside their respective coop. How big this would be depends on how many birds you want to keep and how big their outdoor space would be.
Partitions could be as easy as putting up some fence materials to separate the flocks, or as fancy as building walls.
In two weeks I am getting a 10x14 coop that I ivide in two halves, each 10x7, for two separate flocks, by putting a wall in the middle. Each half is going to be accessible by a door in the 14 ft wall, and each flock will have a run coming off of the 10 ft wall at each end.