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If it's smelly right now. sprinkle a good layer of agricultural or hydrated lime on there (WEAR A MASK AND EYE PROTECTION), then dig or till it in really well. It should help considerably.
Also, smelly dirt floors are often damp dirt floors - NOW, before you have litter and chickens in there, is the easiest time to assess and fix that if it's the case. Mainly, make sure surface water and roof water are diverted elsewhere (ditches, french drains, berms, gutters, etc) and make sure coop and run are not a 'low spot' that stays wet or gets damp coming up from below -- raise the floor with extra dirt or gravel, if needed.
Me, I am a firm believer in softwood shavings in bags from feedstore; but some people use chopped straw, pine straw, dried leaces etc. Sand is common in runs. Search this forum on 'bedding' for more points of view and discussion of options.
Good luck,
Pat