If you properly design and maintain it, it shouldn't stink at all.
That means never over populating it (keeping the number of birds per sq feet in the coop/run setup to no more than 1 bird/15 sq feet of space), keeping everything DRY and very well ventilated and removing the poop load from the coop often.
I recommend the use of poop boards in the coop that are cleaned daily. I scoop the boards every day into an old 40# cat litter bucket with a closing lid. I then compost it and use the compost in my veggie and landscape beds.
Now the compost bins should FAR from your house.

Nothing will clear your sinuses faster than a freshly dumped bucket of chicken poop. I sometimes dump a bucket of fine saw dust over the fresh load and that helps a lot but you can smell it for a day or two after dumping.
As for the run, put a solid roof over it with extended over hangs to protect it from getting too wet. Use a thick layer of wood chips in the run to cold compost the poop load. And make SURE that the entire coop/run setup is on high ground so you never have standing water anywhere in the structure.