Crying or noisy puppies are either hungry or cold. Are they gaining weight? If you aren't doing it already, you should be weighing them twice a day to check that they're gaining. As long as they are gaining weight and warm, don't worry about the peeps they make.
As for the fleece, I would be too worried that the momma will get into the box and lie down on top of the fleece, squishing the puppies. I do this during the day too, but I can't check them all the time at night, so I won't take the chance to do the same at night.
Is the miracle puppy gaining weight? How is she acting?
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