Runs smell either because they have too much poo or are too damp, or (usually) both.
To address dampness, see the 'fix a muddy run' page linked in my .sig below (even if yours is not *muddy*, the same fixes apply, and will greatly help with stink)
Organic matter in the run (such as mulch, shavings, etc) can be a problem if it is allowed to stay there long enough to get damp and poo-saturated, although if you change it frequently or live in a very dry climate it can work ok. Sand is a bit 'safer'.
To whatever extent you can clean the run, of course that will help too.
And, not instead of but IN ADDITION TO all the above (especially you really should try to keep the run as dry as possible), you can till in some garden lime (not quicklime) into the top few inches of the soil, that is usually cheaper than stall powders and works about as well.
Good luck, have fun,
Pat