I do plan on putting gutters in and collecting the rainwater from the coop and run. All of our land runs downhill...there really isn't a level area. Closer to the house is better because there isn't a spot that almost levels out, but shade is a problem. Also our friends said you don't want the coop too close to the house because of smell. But I'm also reading that the deep litter method works very well for smell. So I dunno.
We plan on having the chickens free range the backyard during the day, regardless. The covered run will be for yucky days or when we are on vacation (which won't be for awhile). The oldest 9 chicks are already almost 5 weeks old and the 20 young chicks are almost 2 weeks, so my priority needs to be getting the coop built. They are in a 4x8 outdoor brooder now, which I should have made taller.
I have noticed during absolutely torrential (record breaking) that the area down to the left of where I put the coop in can get really soggy. I don't think it gets too bad where I was thinking of putting them. I like that spot because of the trees. Excellent shade and our back yard gets LOTS of sun.
I'll take a video of the backyard and post it. Maybe y'all will see something I don't.
I have a few thoughts for you.
Roosters crow. They can crow a LOT. Everything from a couple times a day to continuously day and night. I have a rooster that is silent for several hours at a time, but he still occasionally crows at 2 am, 3:30, midnight, 4:30. Sometimes he crows 4 times and stops. Sometimes he crows every minute or so for over an hour at 3:30 in the morning. In the middle of the night. It varies from day to day, so I can't get used to it, predict it, and ignore it. Sometimes I go outside to see what predator he's upset about, and that helps him stop, but sometimes I"m too tired, or the weather is awful. My coop is ~150-200 ft from my bedroom windows, and it's still too close, in my opinion. The rooster still wakes me up. If he did it more often, he would have to find a new home. Unless you run a white noise generator in your bedroom every night, be prepared to hear the rooster(s).
Also, since you plan to free range them, you may want to look at the size of your yard vs the number of chickens you have, and consider the chicken loading for the amount of yard you have available. Don't quote me on this, but I think something like more than 5 chickens on an acre will have them tearing up your entire yard and eating all your grass - it will just be dust after a few months. Also, even if you only have a few chickens, they will dig holes in your yard in their favorite spots and poop everywhere and you'll have to fence your garden and any other plants you don't want eaten. I currently have my chickens in an enclosed covered run due to AI in my area, and I'd recommend even if you plan to free range most of the time to have a large enough run that they can be locked in there for a week or so (due to you taking vacations, poor weather, avoiding predators, etc), and not have it create behavior issues.
The minimum recommendation on here is 4 sq feet of space in the coop, 1 foot of roost space in the coop, 3 square feet of ventilation in the coop, and 10 square feet of run space PER CHICKEN, and the 3 sq feet of ventilation in the coop is for around North Carolina. I live in north Alabama, so our climate is somewhat similar, and I find that 15 square feet run space per chicken is actually much better from a crowding perspective for the type of chickens I have (helps prevent fights and gives you space to put things in the run, which is important to combat boredom and behavior issues).
Here's a link to my open air run that my chickens have been living in all summer in the 100F+ weather under mottled heavy shade. In a few months we'll have a shed coop built, but I could probably have added an open top box (huddle box) in the middle and used this run all year, if I wanted to. Might give you some ideas. I use ~6" wood chips/grass clippings/leaves/dirt in the bottom of my run, it keeps the chickens feet out of the occasional rain that seeps into my run during the occasional deluges. If it were worse I'd build a berm and/or a french drain/swale to keep the water out. I water the run occasionally with a hose to keep down the dust.
https://www.backyardchickens.com/th...-now-i-need-a-coop-please-help.1519455/page-9
There are recommendations for 2 per acre, 50, 80, and 100! 
