I raise dogs so I might have a little input here. Is this area used strictly for them doing their business or are they put in there when company is over etc. Do you currently do the poop scoop thing in the run?
I most all my runs set up the following way. I take and dig down between 3 and 4 inches and place 3/4 stone in the bottom. I then take a plate compactor and pack it as hard as possible and try to keep it fairly level as well. It doesnt have to be perfect. this usually ends up taking the level down about an inche or so. I then take and put 2 inches of crush and run and pack it as well. I end up with a nice hard surface that isnt muddy but isnt hard on the dogs pads. I also can take a hose and wash the poop out the back where I lime the heck out of it.
I actually just built a set of kennles for a friend and instead of the crush and run I ended up using polymeric sand. Which i compacted and then lightly misted water on it until it was wet. After it set its like concrete almost. Still not too rough on the pads. I am thinking of redoing my pens this summer like this.
Keep in mind that most of my pens are in full use most of the time and I see no adverse effects from using packed stone.
You can actually just put a few inches of crush and run in there and pack it really well you dont have to go through all the extras I do. I just tend to do things well done sometimes lol If you have any ??'s you can drop me a email at email@example.com