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I have a fairly small run as well 6'x8'. What I do is I remove some of the dirt, mixed with shavings, and spread it on my garden beds. It's wonderful stuff, all nicely tilled. I then take a bucket of fresh dirt, usually mixed with weeds, turf, grass, worms etc., and place that in the run. I then add some fresh shavings as well. They help absorb the moisture. (I also throw in some DE about once a week.)
The birds love the new dirt to pick through, and find the bugs and worms. It keeps them amused. I do this daily, and the run is not smelly at all.