I am not sure keeping the puffer will be hard per say Niki, or that you even have to be doing water changes like that.
Water changes shouldn't hurt or freak out your fish as long as the makeup water is balanced to the water in the tank (same temp, same PH).
Again, Cindy may come in with totally contrary information, but I doubt I am to far off is all that I am spouting is good aquarium husbandry practices, regardless of the fish.
Will it be hard, what is hard for me may be easy for you, or vice versa, I really don't think keeping an aquarium is that hard, people talk about advanced aquarists, and seem to think that label takes time to get, but consider this, person in the hobby after 10 years finally gets it through their thick skull they should do bi-weekly water changes (on a standard sized tank) and things click into place and they start having phenomenal success. Person in the hobby for 1 month reads a lot of books and studies stuff on the internet, and does it right from the get go... phenominal success. I consider both people to be advanced, yet one tool longer to get there.
Point is, you may have no problem what so ever in a 3 gallon tank, then again, maybe it will make the puffer feel cramped and he simply won't like it, that is a cindy question.
As far as getting oxygen in, you can go several routes. Air stone is the old way of doing it, Bio-Wheels are the new way of doing it, or, you can go the elegant way and plant your little tank and let the plants produce oxygen for the fish. (my favorite way.) (note: don't use a bio-wheel, air stone, or spray bar on a planted tank, it will strip out CO2 and reduce plant respiration.)
to get out waste, you can run carbon, purigen, or any number of products on the market right now (like chemi-pure pads), or you can again, take the elegant route, and get some live plants.
Oh, you asked about snails. You may need to breed them on your own. if you set up another tank with apple snails or any type of pond snail, you could easily produce food for your puffer. I don't know if there is a commercial source for frozen snails that would be small enough for your puffer, or again, if the puffer even needs it, I am not sure how different these guys are from saltwater fish.
Oh, btw thanks... I was looking at dwarf puffers on the net and I think I am going to have to set up a tank for a pair of figure 8s... or at the very least (if I go for the easy FW, some red eyes.)