If you need to secure your root domain (“www.mydomain.com” and/or “mydomain.com”), a standard RapidSSL certificate can cover both of these versions, but you must create your CSR with the “WWW.”
So: generate the CSR specifying that the Common Name (Domain Name) is “www.mydomain.com”. RapidSSL will then automatically include also “mydomain.com” in the certificate you'll receive. Covering both versions has no downsides and enables more flexibility.
If you want to cover a different subdomain, such as “mail.mydomain.com”, then this does not apply: in this case just generate your CSR with the exact subdomain desired.