That might be all very well but Personally I would not take the chance - keep them separated until you can see a vet and have the little one checked, I am sure kitty is OK but...you need to look out for Fluffy until the Vet gives the all clear.
I would keep them isolated until you get him to the vet. Better safe then sorry. Shots are great but don't protect against everything! I know you're probably dying to have him integrated into the household and play and cuddle! It's hard.
It would be cheaper to run out and pick up a cheap litterbox than to have to pay vet's bills should Fluffy get something from the kitten. Or use a cardboard carton with a thick layer of newspaper under the litter. If I were you, I wouldn't chance it.
Some grocery stores sell disposable litter boxes, or you can use one of the cardboard flats that grocery stores stock canned sodas from - just put something underneath the box so it doesn't soak through to the floor. You really don't want a new kitten sharing a litterbox or food & water bowls with your existing cat until you're certain it's healthy.