Unlike virtual subdomains, ‘real’ subdomains have their own independent home directory, can have their distinct mail setup, users etc. On the other hand, they take up one of the available virtual server (domain) slots on your account.
To create a full featured subdomain, set it up in Virtualmin as you would a regular domain, i.e. click Create Virtual Server and enter e.g. ‘sub.domain.com’ as the Domain name. This will create a new virtual server for the subdomain, with its home directory at ~/domains/sub.domain.com.