Don't feel bad. You and your wife are certainly not the only people to buy a snake from PetCo and get the "free case of mites" deal. Here's a link to a write-up on mites to understand your enemy....

http://www.vpi.com/publications/the_...of_snake_mites

Personally I'd have the little one on plain white paper towels for a substrate until you know the mites are gone (after another month or so of no hatching/new mites). I like the Viva brand for it's clothlike softness. If you use natural hides I'd switch over to something in plastic that can be sterilized and cannot harbor mite eggs. I'd order P.A.M. simply because killing off the adult mites is one thing but if you don't get the eggs (much harder to kill than the adults) then in about a month or so you are going to have mites again.

Treating the snake, dealing with the shed, being pooped on are just things that happen so don't worry on that. Just like we have to deal with our kids when they are ill and don't want us fussing over them or giving meds, there is just stuff that has to be done with snakes - so best to do it calmly and just get it over with quickly and efficiently.

You might want to consider a good, fine shred aspen once you go back to natural substrate. I buy ours from a store that stocks bedding but no snakes and have yet to see a problem with mites coming in on the bedding. Do watch yourselves though, if you visit pet stores or snake shows and handle snakes, that you don't become the ride home a snake mite utilizes.