We also use a deep litter. Hubby built the pen attached to our garden shed for one wall, is about 8'x10' enclosed with poultry wire with a large 5'x 2 1/2'x 3' wooden box (for nesting)with door opening attached to shed wall about 18" off the floor. Inside the nest box is about 6" of paper shreds and in the pen area I spread out one bale of hay on the ground, made for 8+" of base. found a large board about 2"x12"x8' long and put under the nest box to deter any ground burrowing pests. This sticks out far enough to put their feed and water buckets on and seperate from litter. These buckets are 5qt ice cream buckets. Once in a while I've fished out a stray straw or feather, but is usually clean. I empty and refill every few days and the feed is kept only about 1/2 full. This provides several days of feed and have had no waste yet with these buckets. I did use trough feeder and self waterer, but most feed was dumped and wasted and didn't see anyone trying to drink. Now they do.
At first when I did dlm, I did it backwards by putting in alot of litter and taking out the dirty parts. Then in a light bulb moment, I realized my error. So now, every few days I use a pitchfork to turn, fluff and toss the litter, depends on how bad it is. I check the nesting box (hinged roof) and clean out any dirties onto litter flooring. Adding new as needed to both box and pen. Paper shreds, shavings/bedding whatever I have or can find. I don't have a stink problem. But my chickens only stay in the pen during the night and are usually let out in the am and we close the door after they've gone to roost. Since this will be our first winter, we'll see how it works to also provide some heat.