If you walk into my house, even the room where the chickens are, you can hardly smell them. If you walk into the lobby of the stables when we have chicks in the brooder, it hits you. Why the difference?
CLEANLINESS!!
I put a deep bed of shavings in the brooders and cover it with an old sheet or plastic cross stitch squares to give them footing and keep them from eating the bedding. After a couple days, take the covering out and they have the shavings.
At home, I put the feed on one end and the water on the other. At work, it starts that way until my day off (I have 3 in a row)and lazy people stick them next to each other. (don't have to take the whole top off, just lift the end)
SPOILED, WET CHICK FEED SMELLS WORSE THAN POOP!
I also remove any bedding that gets soaked around the waterer daily. Also, if there is spilled feed, I'll scoop that out as well, so it doesn't get sifted down under the bedding. Fluff up the bedding and add a handful or so of fresh shavings.
After a few days, I put the waterer up on a brick to raise it. I find that if the brick is the same size or a little smaller than the waterer, they get less shavings in it because they can't climb up on the platform. Same with the feed.