Deep litter..What am I doing wrong?

I don't have a coop with a floor. We have covered pens directly on the ground. We have some hooped and covered with tarps (3 of 5 destroyed during Hurricane Florence last week), some covered with flat tin, 1 is a truck topper with a sheet metal bottom attached to 2x4 wire for a pen that was roofed in chicken wire, now not...

So we just got inundated with inches (FEET? - not sure exactly how much we did get here) of rain. That hit the ground once the 3 tarps were shredded... Birds were wet and there was some ponding (not much) before the rain stopped... The grounds of these coops has previously been yard/pasture grass and DLM. They DID drain exceedingly well. My granddaughters (ages 7 & 8) helped me and we removed a 2x8 section of compost about 4" deep (broke up 8" deep, but left loose stuff in bottom of "trench") from Coop 1 behind our house. That was work and as far as we got. Then started adding yard debris - weeds, grass clippings, sticker plants, pine straw, pine cones, pine branches etc... 1st 3 pics show the day that tarps were removed by wind and birds wet; pens muddy.



Then 1 pic showing what coop 1 looked like when we started removing the wet "compost" (previous bedding)... No close ups of very sandy compost materiel. 1 pic showing (not very well) the "trench" & 1 pic showing the bags with removed compost (took 2 days to pick up and move those bags up to tires I've set up for planting Hardy Kiwi this winter).



Then some pics, the 1st day, after we started loading the pens with live materials removed from around the house, backyard and chicken areas. These include grass, weeds, flowers that had been dead headed, pruning from the Azalea bushes, pine straw - both long and short and all the fronds from a Mimosa tree (it grew back from suckers on the stumps where two trees removed, guess we haven't killed it yet)... It didn't take long for the material to get spread and pressed down flat! Of course, using packed 50# feed sacks really isn't a lot of material, all told, though it sure does when you are removing it, filling the bags and then moving those bags.



and I just finished a couple more pics showing a few days later...


and then more materials...



I have another ongoing thread showing these same pics as we go along. BY (Back Yard) Coop 3 was partially covered by the original tarp & also had some boxes/crates for protection. The roof of the coop hasn't been "hooped" yet and I can't stand up in it. It has not had materials added at all yet (the chickens have been in it since July - when it was a veritable forest - hadn't had chicken in it since late 2015) as I wanted to get it hooped and dug out a bit - but that didn't happen yet, so may add a few bags of material to it today - even though pretty much dry.