My 2 cents - DON'T use paper towels. I used to do this, and then I found one of my hatchlings who was in the process of eating one, and the paper got stuck. I gently pulled it out and he was okay. The thing is, he could have choked and died. You see, pinkies kind of stick to the paper towel. I am not the only one that this has happened to. So if you do put a paper towel in there, you have to sit right there and watch the whole time. I like to leave them alone (and clean their cage) while they eat, like many do. So no more paper towels for me. I do use them to wipe up however.
More on topic, you can use the container for others, after wiping out, if your sure none of your snakes has parasites, mites, etc., or you could spread a disease to all of them. And who can be sure of that? It is, of course, safer to use individual containers, but I bet most people don't.