If you already have a multi-domain SSL Certificate, you can simply start the re-issue process and add the corresponding number of SANs to your Certificate. The regular checkout flow will prompt you to purchase additional domains.
Note: Starting May 3, 2016, Comodo certificates can be reissued for any Common Name at no additional cost.
The additional domain names can be changed completely during reissue as well, e.g. from domain.com to example.net.