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A lot of what you do in the run depends on how much room they have, how good your drainage is, and your weather. If you have minimum space, you will probably need to do something to manage the poop. If they have enough room, you probably don’t need to do anything. The poop will be spread out enough and they’ll scratch it enough that it will just disappear.
I can’t tell you by square feet how much room is enough. Like everything else with chickens, it depends. If your run is located where the water drains from it and does not set in it keeping it wet, you need less room. If your drainage is fixed so rainwater does not run into it you are better off. I put mine on a slight rise and put in a swale to divert rainwater runoff around it. You maybe can also use a berm to divert runoff, depending on how it is situated. And of course, it depends on how much rain you get. Even if it is covered rain can blows in from the side. It is really hard to keep a run dry during a wet spell.
Some people use different things in their run like wood shavings or straw and it works out. I don’t like to use anything organic like that because it does hold moisture. But if you are willing to rake it or replace it regularly, it can work out. Mine is just bare dirt. Some people fill it with sand to make it easier to rake and the sand drains pretty well. The problem with that is that the sand can disappear down into the dirt over time and needs to be replaced, but it is a great surface for the chickens. They love to scratch in it and dust bathe in it, plus they can use it for grit.
I don’t use wire on the bottom for predator protection. Instead I put an apron around it. If you take maybe 18” of hardware cloth or that 2”x4” welded wire fencing and lay it horizontal around your coop and run, you can stop digging predators. Attach it to the bottom of your coop and run so nothing can get in there. You don’t have to bury it but a lot of people remove the turf and put that back on top to hold it down and hide it. The idea is that a digging predator starts to dig, hits the wire, and does not know to back up. It’s pretty effective.
Whether or not you should lock your chickens up at night depends on your confidence in how predator proof your run is. I did not see you build it. I don’t know what materials you used or your building techniques. I can’t make that decision for you. Practically any predator, including foxes and raccoons, can be around during the daytime but they are usually more active at night. I think it is a good idea to lock them up at night for the extra protection, but if you have confidence in your run, you can leave the door to the coop open. Depending on the size of your coop and how many chickens you have, you may be able to leave them in a while in the morning or you may need to open that pop door pretty early. My coop is plenty big enough that I don’t have to let them out at the crack of dawn every day, but if you have the minimum sized coop, you may need to. We all have different situations and we all manage them differently.
Even young chicks can easily fly over a 4’ fence. They question is if they will. Many people keep chickens inside 3’ high fences without any real problems, but I have had them escape the run with 5’ high fences. It just depends on how motivated they are to fly over it. Some chickens just seem to have the urge to roam and explore new territory. Some are more content to stay put. Part of that depends on the personality of the chicken and part depends on how much space they have. A hen trying to avoid an amorous rooster or trying to get away from a pecking order fight can be pretty motivated.
It also depends on the type of fence. If you have a solid rail on top of the fence, it is pretty normal for a chicken to fly up there to perch. You don’t know which side they may hop down on. And once they are out, they don’t know how to get back over the fence. If the top of the fence is wire where they don’t have anything to perch on, they are a lot less likely to hop up there.
I can’t give you hard and fast answers. Chickens are living animals and you never know what they will do for sure. Each of us have different set-ups and circumstances, different goals and risk tolerances. We all manage them differently. You have to make the decisions on what to do.
Hope this helps some and once again,
