Mine will scratch to cover their food. They all do it, so I'm thinking it's instinct.
One thing I would call your vet and ask about, as Scott and Chip have already been exposed to each other is potentially getting the antibiotics and treating them at the same time. I'm not too up to date on URI's but I believe they are contagious.. so it may be better to see if they can be treated simultaneously especially if Scott is showing symptoms too. If you end up treating them at different times they may just pass it back and forth which will result in a much longer treatment period and ongoing issues.
A suggestion about the litter box issue is to put multiple litter boxes around the house. I'd put one, at least for a few months, in the area close to where they are pottying inappropriately. As long as they're kittens, keep in mind they're babies and may not make it a long distance to potty (just like kids, sometimes they don't realize they have to go until they *really* have to go)..a little later on, when they're a bit older, you can reduce the litter boxes to one per floor, possibly, although I'd also keep one in any room they may be locked into for any length of time.
A note on the food, water and litter box.. they should ultimately, all three, be in seperate places (according to cat behavioral studies).. a cat's natural preference is for them to be at least across the room from each other. That being said, mine have them all in a relatively close proximity and we have no issues with it..
A number of people (and books) recommend treating a soiled area with a product called Nature's Miracle. I've been pretty successful with just steam cleaning, but I have an industrial strength carpet steamer so, that may be why.
One other thing, I noticed that you mentioned Banfield. I have all of mine on plans at Banfield, and I swear by my vet there. He's awesome. Keep in mind, though, and you'll have to contact them about this to find out the details, that their plans are preventative maintanence, not insurance, but much like insurance, I believe that when I talked to them about a cat having an issue and putting them on the plan, they said that there's some problem with ongoing illnesses, but it may have been that they won't use things like included blood tests and so forth to detect those issues.. (my vet, however, has and will do whatever he can to reduce the cost and if he can use something on the plan so it's free, he'll do so). He doesn't necessarily abide by what Banfield itself says. The point there was, I'd check into what they cover if one of the kits has a chronic illness. The great thing, and the biggest reason why I have mine on it, is because I get free office visits.. CRAP!! I stepped on you, it's time to see Dr. B. Did I just hear you sneeze??? Off to Dr. B. Is that vomit? Who vomited? Off to see Dr. B.
Why are you crying while you're in the litter box? Why aren't you eating, why are you shivering.. is your paw hurt? Yes, needless to say, I'm a pain when it comes to the babies, but Banfield is an excellent source of preventing (and saving me money). I don't even believe in yearly vaccinations, but even without those, I still save a ton of money taking them for checkups. I'm probably a bit more over the top than most, though
Anyway... congrats on the little darlings!!! Kitties are wonderful!!!