I always put towels under the fleece. It all needs to be changed every three days and washed at 60 degrees. You will need to remove poops at least twice a day. Personally, I think fleece is a lot better then hay as bedding as so much hay gets wasted.
I swapped from sawdust to fleece and I love it and my piggies do too. I have to be honest I don't use anything normally under it but if I do I just use newspaper. I clean thoroughly every 2 days though with disinfectant & all
People say they put towels under the fleece, which is good, but in my experience, towels make the smell stronger. I just put fleece in the cage. But you have to spot clean with a mini broom shovel thing, twice a day-in the morning and at night. And you have to change the fleece at least once a week, maybe two times, if it smells really bad. I also used a special paper bedding thing, but I didn't like it because it would smell, was hard to clean, left stains, and after a certain period of time, would start to mold which was disgusting! So, in my opinion fleece is the best, but it's what you feel like. I've tried fleece, bedding, and a combination of both, and I liked fleece best! The other thing that I like about fleece is that there's so many colors and patterns! Hope I helped! =)
You can put puppy pads under a fleece. I used to do that but now I use towels.
Lots of people seem to buy stick on Lino tiles from pound ships and put those in their hutches to make a wipe clean base. You could try that? I would personally use something more than just hay on top of the waterproof layer but only because hay isn't very absorbent and so you have to change it very frequently so the piggies aren't walking or standing on damp hay which could cause fungal infections.
I have also used (and still do in some cages) Fitch bedding. I like that. Fleece is less messy in that it can't be kicked out the cage but Fitch will usually go a week between full cage clean outs and you don't have to sweep poops twice a day.