I buy the bagged Pine medium Flake wood shavings from TSC, and check them thoroughly to see if they're damp before purchase. That's what I use in my brooders. If I hatch chicks, I might use papertowels at first for a day or so, but then the wood shavings. If I get chicks in the mail or from the store, I use shavings, cause they're not newborns. I found that sprinkling their food with grit, or mixing a small amount into the feeder for a week or so, then providing a separate grit container after that gave me comfort that when they eat the shavings (no way around it really), they'll be able to ground them down and pass them out the other end. If you think about it, when they're raised by a broody hen outside, they would naturally be eating grit anyway, and anything else momma told them was good to eat.
I haven't really had a problem keeping my brooders dry, and that's the key to preventing growth of mold and many bacteria. I found that if, when the chicks are sleeping in their pile, they take up more than 1/4 of the brooder space, IMO the brooder is too small, and the shavings may have a harder time handling the manure load (drying out the poo). For eggers, which is what you have, I either keep a 1" fluffed layer and change them every day or so (they compress almost flat) or I keep 2-3" deep and change them every few days, or once a week, whenever they seem like there's a lot of poo. I place my chick waterers up on top of inverted glass pie plates or casserole dishes to keep them up off the litter, and put shelf liner under if needed to prevent them from sliding. Sometimes, depending on the waterer, I'll actually place it inside a pie dish or other container right side up so the dish catches any overflowed water. Gotta keep it dry and change the shavings asap when they get wet.
I hate chick waterers! They are always getting nasty. At 4 weeks, I transition my chicks to a horizontal nipple waterer (I put the nipples [Roosty's brand orange ones with a backing screw are my favorite for thin walled containers] in a 1 gallon pretzel or cheese puff plastic container from Rural King for example, make sure you make a small hole at the top to prevent it holding a vacuum, and test for leaks after you get the nipples into the container). I found 4 wks is the youngest they're strong enough to use them, but I've not had any trouble training them. I peck the metal posts with my finger "beak" to let the water out. There's always one chick who's curious enough and thirsty enough and leads the way, and the others learn by example. I wire these waterers to the side of the cage so they don't tip over and elevate them on blocks of wood or inverted bowls and such depending on the chick height. I love horizontal nipple waters! They give a constant source of clean, fresh water, and no more leaks in the brooder or constant water changes!!!
I don't know what's wrong with your chicks. But if you're feeding amprolium (CORID) to treat for coccidiosis, feed them unmedicated chick starter and do NOT feed them any type of vitamins (Nutridrench, Rooster Booster, etc). There is a specific B vitamin (I think it's thiamine?) that the coccidiosis needs to live, and the CORID removes that from being available, which is what gets the coccidiosis out of the chicks's system. Once the chick is stronger from not having to deal with coccidiosis, they will deal with it again (it's everywhere outside) and because they had a chance to strengthen their bodies (thank you CORID), they will use their immune response to not let it affect them the next time they encounter it. You just have to get them through the first exposure and build up their immune response without them being overwhelmed by too much of it, and then for the rest of their lives they'll be fine, unless they encounter a different strain (happens occasionally but not super often is my understanding), in which case the process repeats itself with the new strain of coccidiosis, and you can re-treat with CORID if needed. This is my "I'm not an expert but did a lot of reading and treated my chicks a year ago" synopsis.
I hope your chicks continue to do well! Sending you best wishes!!!