I really don't have trouble with smells or hygiene, but my secret is not all that useful if you are trying to raise quail for anything other than eggs and pets: Low density. At most, I have 8 or 10 in a 100-sq-ft area. It's shaded by tons of trees, so they also constantly have tree leaves falling in and adding carbonaceous material to help decompose the poop.
If I had a larger number, I'd probably bed them with straw and just mix it up/add more regularly. Still, for truly factory-style numbers, raised pens are probably much more practical. I find in a raised pen that it helps them a LOT to have a sandbox to hang out in. When mine were in brooders, they'd spend almost all day in the sandbox, and it's where they'd lay their eggs too. Kept the eggs cleaner & easier to collect, too. Put high sides on two or three sides of the sandbox though--they'll kick the sand all over otherwise, and you'll lose it through the wire.