We have vinyl flooring over cement. We do use newspapers once the pups are older and the dam is no longer in charge of clean up duty. We have an indoor/outdoor set up with an indoor kennel/whelping box and a dog door to an outdoor kennel on patio brick. I really, really love this set up. By the time the pups are 4-5 weeks old, they are pretty good about going outside to potty. They get better as time goes on and while there's still the occasional peeing and pooping inside, it's greatly reduced and that helps keep things clean.
Our indoor area is divided between a 5x5 whelping box with an attached exercise pen. We put cedar chips in the whelping box, and newspapers over the vinyl flooring in the surrounding pen. With two separate indoor areas, they pick one for sleeping/playing and one for a bathroom. So when the pups do decide to pee and poop indoors instead of going outside (which is usually at night) they consistently do it in their designated bathroom area.
Oddly, we've had some litters that preferred to sleep and play in the cedar chip filled whelping box and use the open exercise pen for the bathroom, and others that preferred to sleep and play in the exercise pen and used the cedar chips in the whelping area as a litterbox. Either way it works as the pups are sleeping and playing away from where they pee and poop, and the cedar chips help keep the area and the puppies cleaner and smelling fresh.
Here's a picture of our indoor set up.