Multi-domain certificates secure up to 3 SANs by the default price. You can purchase up to 97 additional SANs during the initial purchase of the SSL or even after the SSL has been purchased.
SAN, short for Subject Alternative Name, is a hostname that is secured by an SSL.
www.example.com and example.com take separate SAN seats in Multi-Domain SSL certificates, unlike Single-domain and Wildcard certificates that protect both versions by default. In order to protect both versions of the domain with one Multi-domain SSL, they should be specified separately during the activation process.
For instance, example.com + www.example.com + site.net + www.site.net = 4 SANs. You would need to purchase 1 additional SAN for your Multi-domain SSL to protect them all. Each SAN comes for an extra fee which you can find on the SSLs product page: