we had one barn built over clay, and UGH with the urine! We put several inches of gravel down, then rubber mats over that, and it's been peachy keen ever since then. We use shavings in the stalls, and the only time it ever smells is right after someone peed....and that's usually gone in a few minutes once it soaks into the bedding.
I use Stable Grid in my barn. I have classic Virginia red clay. I placed a layer of gravel in each stall, then the grid, then filled the grid with bluestone. I've had it for over 10 years. It's great stuff. It drains well, the stalls stay level and they are easy to clean.