Hello .. I would put the coop outside the fence .. then cut an entrance to the coop in the fence.. with a ramp to the ground .. also .. i would place the nesting box in the side closet to where you will be coming from to gather eggs .. if you have a sloped roof .. i would put the perch's on the high side (inside) and nest boxes on the lower side .. i would also make nest boxes inside the coop and (with a cover over the top of them .. but access the laid eggs from a swing down door running the length of all nesting boxes.. ( no need , in my opinion to have a heavy lid to raise to get eggs) \\\ even tho that's what i have myself / just something i would have done differently .. if i started over