Some L-lysine powder added to the kittens wet food might help. You can get it at most pharmacies or health food stores. I would start with 250mg twice a day, perhaps going up to 500mg twice a day if symptoms are really bad. Some people also give a maintenance dose of 250mg/day once symptoms subside. It would be fine to give it to both kittens. I also wouldn't keep them separated because that could be adding to the stress of the sick one, and like Love4 mentioned, stress can be a factor. Plus, the other kitten has likely already been exposed to the virus anyway. He just might have a stronger immune system and that's why you don't see symptoms.
More info for you:
http://www.holisticat.com/uri.html