When we were redoing some stalls that had an uneven base, I pulled the mats and hosed down the screenings underneath, hoping that would make it easier to hack it up and even it out. I had standing water in there for daaaaaaaays, which is probably what’s happening with your stalls, if the smell is bad? Packed screenings don’t really drain.
You might be able to improve drainage with some different materials or with a dry well in each stall?