puppyhood for you mate, I am going through it also, puppys are hard work at times, HAve you got concrete flooring in your run, ie flags or concrete itself???
I wouldn't worry about it to much, the pup will sort his act out with the dirtys soon, how big is your run?? Its hard to answer as I don't know the whole situation??? If he is soiling his sleeping area that is a huge problem for yourself and really needs to be addressed, but if the run is large enough and he is doing his business in the exercise area I wouldn't worry. He will gradually get cleaner as he is bigger, just think of babies