First, I would like to thank everyone for recommending the fleece liners. They are much cheaper than I thought and very easy to spot clean. The smell is always going to be there but at least the mess is minimized.
I have also noticed that Egon is becoming a little more aware of his messes. He hasn't been pooping outside of his little houses. I have an igloo and a shoe box in his day time cage with carefresh in it and a small plastic storage container with a hole in it and holes in the lid with carefresh. He only goes where I have carefresh so I think he pretty much has the hint. Sometimes he goes behind the wheel but I will take that over the entire cage any day. He is about 2 months old now so I would say hes pretty smart. I still get the huffs when I go to pick him up but I am guessing that is natural and will probably always be an initial response.