As far as clipping wings go, clipping one wing is recommended as that unbalances them so that they are not as tempted to try to fly the fence. I suggest that you build your fence 6' tall so that you can walk into it if needed. If you put bird netting over the top, that will protect them from aerial predators. Make it as big as you can allow. Even if you allow free range every day, a run is essential IMO for several reasons: There will be occasions when a predator will find your flock. A secure run will keep them safe. When they start laying, a run will enable you to train your birds to the nest so you don't have them laying eggs all over the yard. Deep litter in the run is definitely the way to go. If you put a nice deep border around the base (6" minimum) that will help to hold it in. You can dispose of all of the coop litter, garden debris, weeds, kitchen waste, basically, any compostable materials can go in here. Your run will be a healthy place where the chickens will spend hours happily creating composte for you. They will reap huge benefit: healthy bacteria and fungi for their guts and for your soil. Beneficial insects and worms for the chickens. (your feed bill will go down while your chickens become more healthy and much less prone to attack by parasites (both internal and external). Your run will never stink. And once it gets going, you can regularly remove buckets or wheel barrows of healthy compost from it for your gardens/lawn.
As far as free ranging in your yard: Poop happens. I consider it to be little fertilizer packets. My dog considers them to be snacks. If you need to do a quick yard clean up, a hose does a good job dispersing those bombs into the soil. Your birds have their own ideas regarding the perfectly landscaped yard: They will put the stinkiest and foulest of their poops on your deck, patio, and front steps. They will dig dust baths in the middle of your lawn, most likely where you are most apt to walk, so that... if you are not paying attention, you will fall into their craters. They will disperse any mulch into the grass. They will eat all of your favorite vegetation. Any vegetation they don't eat, they will shred. Any vegetation they don't shred, they will dig holes into the root systems so they can wallow and dust bathe under that particular plant until it's dead. Deer netting is great for protecting specific areas from their attention. You can cut a 7'W roll in half with scissors to yield 3.5' rolls. It's practically invisible and easy to put up with thin fiberglass fence posts. The chickens will bounce off it, they will run circles around it, but because it's so transparent, they don't think to try to fly over it. I wouldn't use this for a run, but it works great to fence them OUT! Leave the garage door open, or any door for that matter? They will organize a self guided tour. The tour leader will lead them through, as they discuss and inspect each new item they find. they will spend hours inspecting the contents of your garage, checking out all horizontal surfaces for perching comfort, as well as decorating all of those surfaces with poop.
An other good reason to have a secure run: you can let them out for short periods of yard landscaping and destruction, and put them back in when they've done enough damage for one day.
Chickens spend a lot of time on their roost at night laughing at the infinite amusement you provide as you scurry around the yard cleaning up after them.
