Until pups eyes open, I keep layers of newspaper under towels; the towels being replaced with cleans ones as frequently as needed. At least daily. Mom keeps things pretty clean when the pups are this young.
As soon as pups are on their feet, I put a "litter box" in the whelping box. Use pine shavings that come from the local feed mill that are labeled "horse bedding". They are dustier than the shavings I used to get at the pet store, so more absorbent.
As pups leave the lunch bar, I pick them up and stand them in the litterbox. Takes only a day or two before pups have figured it out. I put some newspaper or towels around the base of the litterbox ... as they don't always aim well. This works WAY better than letting them do their messing on newspapers.
For the litterbox, I use a plastic under-bed storage box. Easy to find in stores like Target, Walmart, etc. (my whelping box is 4'X4').
I feed pups in individual dishes; usually groups of 3. Keeps them cleaner & also assures that everybody gets their fair share.
Like Helen, I buy towels and blankets at the thrift shop.