There was a thread on here a few years back that was very similar. I'm not going to try to find that thread though, that would be a challenge. The main difference is that yours looks like you can walk in there, that is a huge advantage.
Wet poop stinks, dry poop does not. It looks like the ground slopes away from that area and you said it stays dry. That makes it possible. Another place poop can be wet is when it builds up. Many of us handle that by using droppings boards. Chickens poop wherever they are. during the day they are often moving around so it probably won't build up that much. But when they are on the roosts they are not moving around so it builds up.
If you put something under the roosts to catch it you can remove it easily. Some people use a sheet of plywood and scrape it, some build a tray and fill it with something so they can scoop it like kitty litter. You can build a hammock or just get plastic bins from
Walmart to set under them. Or you can clean that area out on a regular basis. I'm sure there are other methods to handle it.
Then you need to do something with it. I put pure poop in my compost pile. If it gets too thick it can stay wet and stink and even draw flies. But if I cover it with grass trimming or such or mix it up pretty good I don;t have those problems unless the weather stays really wet for a while. In those wet circumstances my compost pile can smell even if it doesn't have chicken poop in it. That's the way composting works. You can try putting it in your garbage if you don;t want to deal with it yourself or maybe contact your local master gardeners and see if they know someone who will come by and pick it up. Chicken manure is that good in compost.
In any case you will probably have to manage the poop to handle the smell. I don't know how hard that will be for you but it is a common discussion on here.
The only relationship between your roosts and nests is that the roosts need to be higher. As someone mentioned chickens typically like to sleep in the highest spot available. There can be exceptions but if your nests are higher that's probably where they want to sleep. They poop at night so you don't want them sleeping in the nests and giving you poopy eggs.
I use the top of my nests as a droppings board for one of my roosts. The top of my built-in brooder is the droppings board for my main roosts. Some people find that horrible. To me it's just personal preference.
Chickens often like to be in the shade and where they feel hidden from hawks. They also like to perch. They poop wherever they are and some people can be surprised at how well they can fly. Your deck above the coop may seem a perfect place to them to just hang out in. I generally try to suggest you go by what you see, not what someone on the internet like me tells you will happen, but you might have plan ready to put some kind of gate on those steps.
Another important thing is to not crowd them. The more they are spread out the less poop builds up. The tighter I keep mine the more behavioral problems i have to deal with, the harder I have to work, and I have less flexibility to deal with issues that pop up. I value that flexibility the most.
Good luck!