Oh, I could write a small book about this subject.
To start I will tell you what I did in my stalls. I put topsoil over the clay base since it was free, had no more money and suddenly had a horse who needed stall rest. It has worked fine for the last 2 years. Yes, the floor is not even anymore, but over all I like my stalls more then others I have cleaned that were a lot more to put in. It is not perfect but it works and yes I will do it differently next time.
I have really come to dislike mats in stalls. I have cleaned several barns with them and now would never put them in my stalls. They do not allow for the urine to drain. It does not matter the amount of bedding used or if you use a pdz type of product, there is always a urine smell, when cleaning these stalls. Maybe I am just sensitive to it, since the only time I smell urine in my stalls is when a horse has just urinated. If you really want mats, they do make a cushy stall, use the interlocking kind the others move around and create hazards in the stall. I have read and heard that mats also save bedding, but in my experience this is not true. I end up taking more bedding out of matted stalls because the urine is soaked up only by the bedding. Maybe it is just the situation I have, I seem to be the only one that I talk to that has experienced this.
Now, for what I would do next time. I will make a crushed rock base with a stabilizer product on top such as Equustall Stable Flooring System.
. Then overfill this with topsoil or sand (have not made up my mind on that yet) with the bedding on top of that. This seems to have the best of both worlds, they can dig but the stalls will drain nicely.