3 small coops in same run or 1 big coop?

I got 3 wood shipping crates that are 3 x 4 feet, 3.5 x 4.5 ft , and 4 x 4 ft. I broke them down in panels and was planning on making one big coop but realized that unless I am willing to shell out some money for playwood to make it symmetrical, the wood walls would have different heights eventhought the overall coop will be 5 ft tall and the bottom of the coop will be 12 to 15 inches raised above the ground. The top part of the walls will have hardware cloth. Should I make 1 large coop or have 3 different coops? I was thinking that having 3 coops might be beneficial because 1 coop for the chickens, 1 coop for the ducks and another coop for broody duck pen. If I did that, I would subdivide the run into 3 separate areas. I was going to make a run that is 10x15 ft or possibly 10 x 18 ft. Problem is, the bigger the run, the more it encroaches on my dogs exercise area. Suggestions? Thank your help!