Idle curiosity @chickengeorgeto : What do you have to say about the laying flock that has a rooster, or the laying flock that is going into a molt. Do you use layer, or take them off layer b/c of those issues???
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Lisa, how many birds, what is the size of your coop (the indoor portion where they sleep) L x W x H. And what is the dimension of your run L x W x H? You said your run is wrapped in plastic, are the coop/run a single unit? It sounds like you have a ventilation problem, possibly a crowding problem, and most definitely a drainage/impaction problem in your run.
Minimum size recommendation for back yard flocks: 4 s.f. in coop, 10 s.f. in run per bird. Ventilation: 1 s.f./bird in the coop, even in the winter!
Deep litter management if your run is tall enough will, over time totally eliminate the ammonia issue you are having there. It sounds to me like you have things buttoned up too tight.