chickenspugetsound -- is this the indoor area you're having trouble with, or the outdoor run, or both? If the indoor area smells, you need much more ventilation (cut LARGE holes in the walls, screen with hardwarecloth, there ya go) and possibly better sanitation. If the outdoor run smells, it is likely from having too much mud and/or wet organic matter (shavings, wood chips, straw, hay?) out there with poo in it. Removing all organic matter will help, as will doing various things to get the run to be drier.
See my "Big Ol' Ventilation Page" and muddy run page, links in my .sig below, for a lot more on how to address those two issues.
kyrabear, that is a GIANT number of chickens in not much space, and those metal sheds have very little ventilation. If you already have more eggs than you know what to do with, one sensible step would be to get rid of about half the chickens, which would halve your problem right there
If you are going to go on using the metal shed as housing (it will be a problem in the summer, but...) you are going to HAVE to figure out a way of putting quite a lot more ventilation in there, and removing the poo quite a lot more frequently. If there is enough ammonia for your nose to smell, there is enough to be damaging the birds' respiratory systems. See "Big Ol' Ventilation Page' in my .sig below.
Good luck, have fun,
Pat