Well, you've still only had them 3 days, so no need to panic on the food yet.
And, I'm betting she wants to dig, which the hide with the moist paper towel won't allow. The most paper towels work fine for a most hide, that's what I'm using for all of my babies, but not as much for a laybox. I don't think having the carpet is it as much the problem, as it is not having a substrate to dig in.
And another thought, I use vinyl flooring for my gecko enclosures I cut it to fit, from home depot. Easy to clean, fits tight, holds heat well. I love the stuff honestly. Just make sure it doesn't have adhesive backing.
