If you create a new user account with its primary domain as the subdomain it does not create the directory in your "root" account. It acts like its a normal domain.
No you add a new user through to DirectAdmin so that they have their own account logins to directadmin. When it asks for what domain to use, enter the subdomain and it will act like the accounts primary domain. Doing it this way, it will not be a part of your account