As I realise I can not create subdomain (subdomain.domain.com) which will point to domain.com/subdomain, or better subdomain.domain.com = /srv/www/domain.com/subdomains/subdomain Also, when creating user accounts to "limit" which user can access to which subdomain.
You can easily create subdomains in ISPConfig, just create a new website where you set hostname = subdomain and domain = domian.com. Every client can hove more then one website. Or you craete a co-domain and redirect it to a subfolder.