Creating a CSR for multi-domain SSL

Does anyone know anything about multi-domain SSL certificates? I have a site with Media Temple and have bought a certificate from (a GeoTrust QuickSSL Premium SAN). I've created my CSR on my control panel at Media Temple but can only do it for one domain so I chose the main one. However, when I try to enter my details at it asks for all the domains I want to secure but then tells me that the CSR doesn't cover the second domain. I've asked for support from them but heard nothing back and it's getting a bit urgent so I thought I'd reach out here in case anyone had any experience.