I LOVE my stall mats; was fortunate to buy them on sale for $29 each and NO SHIPPING costs, several years ago. They are the heavy ones, 4 x 6'-I have to use locking pliers to drag them around, but others are right; get the good heavyweight ones that won't be curling up, or moved by the horses--you'll be glad you did!
In my case, I left the size of one mat-4x6'-uncovered, and put a good cover of shavings there. So, THAT'S where the horses will pee when in the stalls. My horses aren't in the stalls too much; only during severe summer heat, anytime there's bad weather, and when it's really cold and/or we're having wind or snow in winter--mine is a large barn, and the horses in their attached runs have the 'buffer' of the building for PM shade/wind protection under many conditions, and I have heated buckets that can be moved inside or out in winter. This means that the open areas of the stalls don't get 'saturated'. I pull back the shavings, remove the wettest, use PDZ or Stall Dry, make sure there is plenty of air circulation-all of which aids in keeping severe wetness and/or odor under control. The 4x6' area is large enough that they can lay down there if they choose, w/o lying directly in the pee spot. Works well under my particular circumstances!
Since leaving one 'mat space' empty in each stall meant I had 'extra' mats, I also placed one mat outside in each 'run' at the barn(I have only 4 barn stalls), and in a couple of my outside run-in sheds, in the corners where I have their feeders. I sweep the dirt off them daily; even though they are all fed in feeders, I feel this helps considerably to minimize how much dirt they might ingest while eating. Since I placed crusher fines in the runs(YEARS ago), and that means a certain amount of very fine granite particles(similar to sand) is part of the ground there, I feel this especially helps.In the stalls, I did not 'prepare' the soil, except to re-level it, before placing the mats; I'm sure I'd have to IF my horses were going to be stalled extensively, however.
Margo