As a new cat owner I can certainly commiserate!
Our vet suggested using a rabbit cage for the little one, complete with own litter box, etc. Then leave it in the middle of the room for the other cat to get used to the little one. When the little one is bigger and better able to protect themselves let it out, if not before.
Luckily we didn't have to get to that place because ours worked it out after 1 1/2 days......