The easiest way for me has been to make the changes as soon as I see more than a couple of flies, or the coop gets an odor. I scoop the poop under the roosts, where it is always the heaviest. Just the top 2" layer of shavings. Then I stir up the remainder, add DE, then more fresh shavings back on top and add more DE. Then I throw BOSS and other seeds onto the rest of the coop floor with a little more DE and let the chickens scratch and stir it up. In a couple of hours the flies usually leave and the coop smells like pine shavings. I do this once a month, and it only takes 15 minutes. The shavings are about 4 inches deep and I've only changed half a wheel barrow full in 2 months. I've only had a slight odor on humid days and never see more than three flies in there. Three is the limit I want to see before I do the cleaning process. In the winter I will do more of the deep litter method, but the humidity in the summer makes me want to stay on the once a month plan. The only poop you have to be concerned with is under the roosts, for the most part. A poop tray might make it easier, but I have no problem doing it with a shovel as the pine shavings are left deeper under the roosts (6") to allow scraping the top two inches or so off of them.
I've hear Vanilla scented car fresheners work well though I've not tried it yet.
Hope this helps.