I would house my chickens in a separate coop. We have just adopted a rooster and are building him a separate coop as the ducks are not fond of him -- 1 has adopted him as "sort of" friend; the other three stay well away and the drake would fight him if he went close.
We are in NE Florida and I think that makes a difference in choice of coop. The rooster coop will have 4 walls; our duck coops do not have four walls: they have end walls -- one which includes the door -- and frame long walls with mason ladder and 1 inch chicken wire attached. The walls are very strong, predator proof, but well ventilated for our frequently humid climate. Mine has a tarp that is currently pegged to the ground on both sides to provide shelter from wind and rain coming from the sides. My son's doesn't have a tarp -- he uses pine straw bales to give protection to the exposed side [the other long side is close to shrubs with a berm immediately behind and doesn't get rain or wind.
We get raccoons in the gardens at night and so have to keep our little ones safe in predator proof coops