I have a different take than some on the idea of whelping pens / boxes due, in part, to this article. That being said, mine is not the "only" way ;) And I'll be the first to say that learning is life long, so there will likely be changes, additions, deletions to my concepts as we experience more.
When dam is whelping, I use straw** in a tarp "den". Mamas like to dig to form the nest, so it seems to really fit in well with their instincts. It makes a bit of a mess in my house for that day, but mama is happy, plus it's economical, biodegradable & easily cleaned up / disposed of.
I use disposable blue shop towels to catch and help dry pups (see pic). Others use washable white terry hand towels. Hauled water vs city water may play a role in which method is chosen.
I use an x-pen to form the den, with a plastic folding table over top zip tied to x-pen to support the tarp "ceiling" and provide rigidity to the walls of the den. Tarp goes all the way around (under, over).
Exterior of the whelping den pictured. The den provides a more cave like atmosphere which dams seem to love. It's highly cleanable. I keep gloves, and other whelping needs close by on the nearby dresser.
Dam mid whelp. Heating pad on the straw while pups nurse.
Once she's done whelping, I place new straw** in a zippered duvet cover to form a nest. It's soft and allows for new mama to make some mistakes when learning where to place her feet or body, plus pups hips have some support from the curve. (Here's a short video showing the slight slope) I then cover with plastic (6 mil poly), then absorbent pads (something like this), then a fitted mattress cover (something like this), then the heating pad (for continuous heat), then a fitted twin sheet.
On the very top, I use a rubber underlay to give the pups traction. The one I use was bought in store at Walmart. I tried to find exact online, but couldn't. Like this, but I buy the 56" x 96" or larger. I find the rubber underlay is inexpensive and flexible / easy to use in the nest. It's easily washed, but takes a couple of days to dry so I have more than one. For sanitary reasons, I purchase new ones for each litter. Why all these layers? They're necessary, believe it or not. I change the top layers every couple of days (so have at least 2 of each item on hand). And I change the bottom layers generally once a week. Yup, some liquid works its way down as far as those medical pads, especially while dam is still cleaning out...
Here's a video of the pups on the underlay. (Once link opens, click on video to get full sound and picture). Pups are standing on hind legs to nurse at 2 days old, rather than scrabbling with hind legs sprawled frog-like behind them trying to get a grip without that support.
**It has been mentioned that mites could be a problem with straw. That depends a lot on source, year, geography, etc. I've not had any issues. However, if one were particularly concerned with mites, the same concept can be created using wood shavings... I have done that, too, just found straw easier to work with / more absorbent during delivery. PLUS, straw has a different smell to it than the wood pellets for their potty area, making it easier for pups to differentiate between the two sites.
Picture shown above demonstrates the nest layout post whelping. I place a "pig rail" at the end of the nest to give the pups a safe area behind mom (best to use a pvc pipe for sanitary purposes if you aim to have multiple litters in the same area, but this needed to be done at a time when I couldn't get to town and we're in the process of building a whelping / puppy room that they will be moved into, so it's a temporary fix for now). As they get more mobile, I place the x-pen closer to the nest at the front, too, to prevent pups from falling out of the nest.
I use a heating pad on the floor in case an adventurous pup manages to circumnavigate my barricades. If pup ends up there, it keeps it warm until it can be placed back with the rest.
Once pups are mobile enough that dam is no longer cleaning up after them, I add a plastic sled with wood pellets to the near end of the nest for pups to crawl to to potty.
Picture is of a previous litter using their wood pellet litter box at 4.5 weeks of age. Their rubber underlay cover was drying; I got more of them so I could swap out without delay.
As pups get older and understand they need
to make their way to an area to potty, I move the sled further from their bed area. Again, pic is of a previous litter... Floor *had* been recently washed but was actually wet from pups playing in their water dish. I now use a dry mat pad for the floor when pups are more mobile. Others use vet fleece, which is another excellent product, just not cheap. I also use more pellets at a time. (Life is a learning curve :) ) I'm still researching ideas for a portable water system that is less fun for pups to mess in :p
As always, a work in progress. :)