Hmm... first, are you SUUUURE it's the chickens that are smelling, and not your fly jug? Usually you'd put the stinky-type fly traps (not the sticky-paper ones, they're ok in the coop) somewhere like 100' away, because my goodness can they ever stench up a place. (Whcih is kind of why they work, but, still)
If your *waterers* are getting stinky despite being emptied and scrubbed each day... that's not right. Are they located such that poo and bedding is getting into them during the day? If so, fix that and it'll fix most of the waterer problem. If that's not the issue, try bleaching the waterers and letting them dry in the sun (you can use dishes as a temporary water source). If waterers are not getting anything kicked into them and getting bleached regularly and STILL smell within a day, there is something wrong with your water source and you really need to get your well or tapwater tested, possibly as a HUMAN health issue as well as animal health. For instance high nitrates can cause quickly-smelly water, and that's really not good for you or the animals to be drinking.
In terms of the rest of the coop -- if you can remove the stinky traps to somewhere far, far away for a few days, and the coop still stinks, it's a moisture problem. Do what you can to dry out the coop and runs and keep them that way. Mount droppings boards and clean them every morning (it only takes a few seconds per pen, literally, honest); fix any and all roof leaks and waterer leaks; if you have a dirt floor, consider building it up with gravel so it is higher and free-draining and not damp; rig windows so that rain cant' blow in. For the run, mount gutters on all nearby roofs however small they may be, with downspouts running the water WELL away; trench around the run, not too close to the posts, to help dry the ground out and lead rainwater away; use roofing or plywood or tarps wherever feasible to limit rain going into teh run; if you have an organic material on the ground in your run (shavings, wood chips, mulch, hay, straw, etc) remove it all and either just see if you can get away with bare ground or replace with a load of cheap sand-gravel 'roadbase' mix.
The drier things are, the less flies and stink.
GOod luck, have fun,
Pat