No matter how you cut it, your coop is only big enough for 6 chickens. I would advise against making it 2 level. Short coops are beasts to work with, they lack enough cubic feet of space to allow for good ventilation. I would bump out one wall of that coop, and model it after the Woods style coop. The add on section could be predator proofed with a full skirt, and be left with a soil floor. I would also hang the nest boxes outside the coop. No matter what you do, you need a minimum of 4 s.f. of open floor space per bird.