Good point, Meredith. I put a piece of vinyl flooring under the whelping pen (pen has no bottom), and then towels in the pen layed out flat. This is it until the pups start to eat real food along with nursing (about 4-weeks). Then I switch to pine shavings.I don't like anything for newborns that they can get under or buried by--the puppy rail only helps pups stuck between mom and the sides; it doesn't keep her from lying right on top of a pup she can't see because of bedding.
I normally don't put anything in the box for the first couple of weeks, then place newspapers in after that.