The way you're going to have to set this up, will be to change the user for each domain to the user/pass for your admin. (Panel > Domains > Manage > edit) With this set up, each person will only have access to the domain you set them up for. However, you also won't have acess to it - there's no 'master' ftp account.
As far as the folder you see when you log in as these users that don't have a domain assigned to them - it's just basically storage sapce - by default there's no web-accessable area for them. You can use remapping, but only to sub-folders (could be wrong on that) - so you can't give them full domain control.