Create a user who will have access to the new subdomain.
Create your subdomain. When you set that up you will be able to set up the path to that subdomain, that path determines who "owns" the domain.
example user: bob
subdomain might be: bobs.yourdomian.com
set it so path is /home/bob/bobs.yourdomain.com
That way, when "bob" ftps to bobs.yourdomain.com he sees only his subdomain and none of your other domains or the main domain.