I like my chickens close to the house. We also raised extras to eat in a dog run attached to our house, right under our bedroom window. It was actually funny listening to them learning to crow, with that strangled kind of sound, while we were laying in bed.
If you have a problem with smell or flies, you need to address that wherever the coop and run is. Chickens shouldn't be stinky. Don't crowd your chickens, allow plenty of space. If you can free range, you can maintain grass in your run. If they're confined, I would plan on putting down a thick layer of sand. Sand drains well and it's easy to rake, to keep it clean. I'd also consider roofing the run to keep out precipitation. A poopy run that is wet is one of the biggest causes of chickens being stinky.
Piles of wet chicken poop sitting on top of wet litter in a coop is the other big cause of chickens being stinky. Not crowding the coop and using enough litter in the coop will take care of that. You can also just clean it out more often.
We live in a rural area, where there are always flies around, due to the livestock in the area. Any dog or chicken poop is fair game, also. We use fly traps farther away from the house, to take care of them. I don't normally notice many flies around. Which is good, because I find them to be really annoying.