The key to stink is moisture...if it's wet, it's gonna stink, so good drainage is most important.
My coop has roost boards with PDZ to absorb ammonia and acts as a drying agent, it also gets sifted clean of droppings every 2-3 days.
The coop floor is an inch or so of pine shavings, keeps droppings dried up pretty quickly and so far have only had to change them out once in 6 months.
My run is just soil that used to be grass, very sandy soil on a slight slope so it drains well. Was pretty stinky during the snowmelt when run size was reduced with snow accumulation and sometimes is after days of rain, but usually is odor free. Population concentration is a factor also, run is 8' x 42' for 9 chooks.
Freshly dropped cecal stools will stink(badly) no matter what you use...lol.
