The Creative Cloud app looks at the Creative Cloud files folder in the root of the user folder you are logged into. If it detects there is already one there, it will give you an option to use that content. If you wanted to keep the files separate, you'd want to keep separate user accounts through the operating system to keep them separate. It is not possible to merge Typekit fonts or sites on BC between two accounts. You have to go through setup up the second one again.