I have a box (made in the UK) which I bought 20 years ago and have used for every litter.  I can fully dismantle it and store the pieces until I need the box again.  I've become rather expert at putting it together each time.  Half of it is for mother and babies, with a piece of vetbed in it and nothing else (to eliminate any chance of suffocation). The babies are switched from the box to a pen when they are around 3 weeks old. The box is separated in half with a bar about 6 inches high, and the other half is where Mum can get away from the babes, eat, drink and rest.  I line this half with newspapers.  Since this is Nimue's first litter, I am dismayed by and not accustomed to the way she makes a total mess of the papers, upsetting the dishes of water and food.  Has anyone found a way to prevent this happening (barring putting no papers down at all, but then, should she have to pee - for instance in the night - we'd have an even bigger problem).  Any suggestions welcome! 

Heheh - whelping and rearing puppies is a messy job!!   We had a whelping box which came in 2 sections, one, 4 X 4 with a base and sides which had pig rails on 3, and a low section at the end for mum to access the area but not the puppies get out.   We had a layer of newspaper underneath vet bed.  And a brood lamp over the top suspended via a 'gallow'.   This kept the whole area nice and warm, and dry through the first couple of weeks.    By the 3rd week, when the puppies started to be up and moving around, eyes open, we moved this section into the kitchen and added a second 4 X 4 section, removing the access at the front - the additional section had a hinged door for mum to walk in and out.   This section had no pig rail and a thick layer of newspaper added.

We didn't leave any food in the box for mum and only a shallow water dish in there once the puppies were onto solids, during the daytime.   She ate outside, them inside with mum allowed in once they had finished to clean up.    We were there pretty much 24/7 so there was no need for mum to pee or anything else, in the whelping box.    She was taken outside regularly to get some air, and stretch her legs.    Obviously the newspaper in the box had to be changed ALL THE TIME once they were onto solids and mum wasn't needing to clean them.    And I tended to plan my litters into the better weather, so that at least part of the day the puppies could go outside in their ex-pen to reduce the amount of newspapers needed!!!   Until the box was moved into the kitchen, one of us would sleep in with mum and babies.

I have a bolted on bowl or a hanging bucket in my whelping pen (made of 5 puppy panels surrounded with cardboard, and covered by a blanket).

The bitch can rest in the living room outside the box after the first days, and I sleep in the Livingroom letting her out to pee as and wen she needs (every couple of hours with how much she is eating and drinking.)

I suspect your bitch is digging up the paper due to the discomfort of the after pains which will go on for several days.  this is the reason I no longer use vet bed in first days but use shredded paper and a heat pad.

As pups can't eliminate by themselves initially the paper stays dry, and also soaks up any discharge from the bitch post whelping and soiled paper is easily cleared out and topped up.

At 3 weeks we move the pen into the kitchen where it is extended to double, for pups, at 4 - 5 weeks they are wanting outside where they spend a goodly part of the day, and pen used primarily for sleeping.