If you want to use mutlisite for your domain, you have two options (the difference is certificate counts)
Add all mutlisite domain to one virtual host and request one certificate for all domains, then install it in that virtual host.
If you want all domains to have dedicated certificate (which means other domains does not show up on this certificate), clone the original virtual host and only change the domain, then request the certificate and install it to that virtual host.
This probably aren't the one you want to do, due to it's complexity.
This method means you literally add all domains into one virtual host, apply certificate for the whole virtual host, reload that virtual host. Then as new domains are added, do it again.