Sim, você pode ir para Add Servers > Import Server e há um formulário de importação para domínios pré-existentes no servidor.
Import Virtual Server
This form can be used to bring an existing domain on your system under the control of Virtualmin. Mailboxes and aliases for the domain name, any existing Apache virtual server and DNS domain will be automatically detected. You can also enter the name of a database to associate with the domain, if any exist.
The password field should be filled in with the administration user's current password, if you know it. Virtualmin needs to know each virtual server's password, for use when setting up MySQL or PostgreSQL databases in future.
If the domain has a private IP address, you must enter it at the bottom of this form and indicate that the IP is used exclusively by this site. For name-based websites or domains that only host email, the default IP import settings will work fine
Eu pessoalmente não tentei isso antes, já que eu sempre instalo o virtualmin em servidores limpos, mas pode valer a pena testá-lo:)