I am not a breeder yet, but have thought about the same question. I found a whelping pad, it is like a big blanket, all the moisture passes through it so you would have to have pads or whelping liners under it. But it is suppose to keep the mom and puppies clean and dry while all the moisture goes through to the pads. They also have disposable whelping box liners. Let me know what you think of them. I found both of these at JB wholesale pet supplies. Here is a link for both of them.
http://www.jbpet.com/Shopping/catego...BoxPads&page=1