I found the best thing with the litter trays is to turn them into food stations - as unhygienic and all as it sounds! When you use Vetbed or fleece, the hay needs to be contained somewhere, which is where the litter trays come in so useful. I used the Hi-Back litter trays for rabbits, which are about a foot square, and just put lots of newspaper and hay in it with a hay rack above. Given that piggies pee and poop the most where they eat, it's fair to say that it works out well in most cases. The pigs still pee everywhere else of course, but many of my lot have taken to peeing as soon as they get into the hay trays. And there's just no point in trying to train them to poop in one place! rolleyes
I did use carpet in my C&C for a few months. Worked fine for me at the time, four pigs in a 4 level 2x4 so not much concentrated mess and four very tidy piggies, but I wouldn't go back to using it again nor recommend it to others. Fleece and Vetbed are my favourites, I switched to fleece full time in October 05 (having dabbled with it on occasions before), so three and a half years now...haven't looked back!