The way I determine height inside a coop is to determine where the floor will be, the top of the bedding if you use bedding. Make pop doors and human doors high enough so the bedding doesn’t get scratched out.
Position the nests where you want them, taking the bedding into consideration. Position them for your convenience, the chickens won’t care unless you have Silkies that can’t fly. If you have a bad back you may want them up off the floor so you don’t have to bend over to gather the eggs. If your coop is height-challenged you may want them really low.
Next put the roosts noticeably higher than the nests or anything else you don’t want them roosting on. Chickens normally like to roost at the highest point possible as long as you have sufficient roost length. I usually use 12” minimum height but if you have a tiny coop 6” may be enough. For different reasons it’s often best to not put roosts any higher than you have to though most chickens can get up a lot higher than many people think.
A coop needs decent ventilation without creating a wind tunnel inside. An easy way to accomplish this is to have openings up over the chickens’ heads when they are on the roosts. Roof vents and cupolas can accomplish this but openings at the top of the walls, especially if you have an overhang to keep rain out, is a good way to accomplish this. I don’t know how height-challenged your coop will be.