Fleece washed in the following method has no smell whatsoever. It needs to be washed in hot water. Personally, I try to use the "free" types of laundry soap. It worries me to think of using perfumed products for the purpose of fleece bedding. To me the fragrance and other additives seem like they would agitate the skin and sinus of piggies living on it 24/7.
Fleece needs to be washed with a small amount (about 1/2 cup) of chlorine bleach, such as Clorox. This is for all colored fleece. Fleece does not fade with bleach as long as it is placed into the water before the fleece. I have a tie-dye piece for a year and its been bleached every time and still looks bright. Using non-chlorine bleach will not kill the bacteria.
The bleach helps to kill any bacterial build-up as well helps a bit on detergent build-up. It's important not to use too much though, as bleach on the fabric of clothing for even humans can cause serious chaffing. If one chooses to use more bleach, I would recommend strongly to do an extra rinse cycle.
Finishing with a small amount of vinegar in the rinse cycle (about 1/2 cup) will finish cutting detergent build-up, reduce static and fluff up the fleece like new.
Personally, I don't like using towels under the fleece really. I do urge you to bleach out the towels if you are going to use them. The bacterial build-up would be immense because they are going to absorb the urine, but never dry out.
My own favorite is to use polyester quilt batting or hospital pads like these: http://stores.ebay.com/petnvet
I lay down a super thick layer of packaged polyester quilt batting (about 2-4 inches) and put the fleece on top.
The urine gets dispensed quickly throughout it and it's basically never wet. My pigs use the area that has this thick batting as their "resting place". I do this on my upper level and it took a month before it finally started to have any kind of smell and I decided to remove it to wash it. (I simply changed the fleece weekly) The batting is cleaned by laying it in the bathtub in hot water and bleach. I soak it for an hour and then just drain it out and lay it on the patio to dry the rest of the way. Plain quilt batting would never take a washing machine or dryer (except a spin dry in the washer) and it would bunch up and be ruined. That's why I wash it somewhat delicately. Since it's only to remove the urine there isn't a need to agitate it in the washer anyway.
On my lower level, I actually sewed up a comforter using fleece. I love it. I have no odor, and it's super easy to change, and to wash.
Hope that helps those of you with odor problems. I say don't be afraid to try different things for the absorbency level, and also to test out different fleece types. For example, I've even found that simply using a quadruple thickness of fleece can make a big difference in keeping things "high and dry".
Some people are averse to using chlorine bleach and prefer using "Oxiclean". I'm sure it works as well, since I love Oxiclean myself for cutting odors out of my kitchen handtowels. Soaking in it makes a huge diffference.
