By default, the last domain (and any subdomains) configured, will be the one which will work for Webmin & Webshell (and Adminer, if it's included). To change this behaviour, you can adjust the hook script, or simply rearange the order of your domains and put the one you want Webmin & Webshell available from, last.

Following these directions, I've kept my domains for Webmin and Webshell as the very last line in the confconsole.domains.txt config file.  However, every time I add a new line (at the top) for another website I'm hosting, I get certificate errors because Webmin and Webshell start using the most recently created cert.  It's not a problem for me as I'm a one-person shop and I recognize that I've just added a new certificate, but this may be an issue for others.