You should install the Certificate via the SSL option within the Domain. The option for adding a certificate via the Server option is mainly for securing the panel. You can copy the Certificate, CSR and Private Key and use them in the domain - you don't have to reissue the certificate.
Having said that, you can go the the IP Address section, and assign the certificate you installed in the Servers section to be the default for a particular IP. If you do so, you may then get the option to select that certificate from within the domain settings itself.