New litter advice for first time puppy owner

So we had a dog get accidentally get pregnant. Our first time with a litter. She’s a full blood frenchie with a corgi. There are 3 of them now. 2 didn’t make it. Question is. They are like almost 6 weeks old. Have them inside. What do you all do with the smell? Constantly change puppy pads and blankets. And in a big caged kennel. But they just go to the bathroom all over. lol. We’ve always had just 1 puppy at a time when we would get one. . But they were always older when we got them and then house trained them. Being somewhat newborn. We are at a loss of how to keep the smell down. Thanks for any help.