I vacuum around the giant crate the wee peeps are in, well not so wee for me, but I really don't mind at all. Part of housework anyway. I do have hay and wonder if I should rake up what is out there right now in the hay barn and use that tonight, they may like that too but I worry they will try to eat it and get something stuck. I have always used pine shavings for everything, chicken coop, brooder crate, horse stalls....never had a problem with it and don't mind cleaning it up either.
I also put our peep food and water on a brick so it stays off the crate or outdoors and they can get to it a lot easier that way.