I never had an issue with smell prior to winter in my chicken area. I do a deep litter method on the floor and a poop litter for their roosts. I have to scrape the boards every week, strain the poo from the stall dry and add more shavings but it was fine. But since winter has hit, I'm having a harder time. I asked Sarah when they came to test my birds what the problem was as I hadn't changed anything. They said that even though I have ventilation going from the ceiling into the garage, there isn't enough cross ventiation when the window is closed. I never had issues last year from their small coops or their room during the summer with smell. It's only with winter and window closed that I am getting it.
So my brother is going to bring over a power tool (cant remember which one) to cut some holes into the wall going into the garage area for ventilation. I suspect once that happens, smell or rather the ammonia that is associated with chickens, will go away. I can't stress enough the importance of ventilation. I truly, truly, truly thought I had enough and I didn't. In the summer when I assumed it would be worse, the windows were open with a fan going so I had great air flow. I just don't have it during the winter yet. So I go out in the mornings now when it isn't too cold and open their window and make sure i close it at night for bed.
Another thing you can try is putting in a couple of those register vents intended for the floor in the house on opposite walls of the coop near the roof. That's what we did in the new coop, and so far it seems to be working nicely. Bob cut the holes with a jigsaw, just put the vent up, traced the hole, and started cutting - and they can be opened and closed, so if it gets too cold or windy I can close one or both. They don't come with screws to secure them, but you can drill through the frame and put little screws in to hold them in place.