Emma has an x pen on carpet that she is in all day and most nights
(yes, we sometimes let her sleep with us!)
I bought a waterproof crib sheet for baby cribs that goes down underneath it. I went to the fabric store, it comes on a roll and is about 48" wide. I got two yards. It's flannel on one side, and soft waterproof rubber on the other. We put the flannel side DOWN on the carpet, with the waterproof one up. Then I bought a couple yards of some different flannel fabric that we put on top of it. If she dumps her water bowls or has an accident, it's really easy just to pick up the flannel cover and wash it, and wipe down the plastic crib sheet. She has several covers since flannel is so cheap, many with paw prints, poodles, and bones on them. It makes for a very cute and easy to maintain little room for Emma!
Oh-forgot to add that the waterproof sheet can also be machine washed and dried, so it's a good deal all around.