Generate a certificate request

Domains > Select your domain > Certificates > Add New Certificate .....
Enter the necessary data and then click on "Request"

Upload/send the CSR to the issuing Certificate Authority and wait.

After you've received your certificate go to "Server > Certificates > Add New Certificate".
requires: key, cert and CA cert
You can either upload them or paste them

After that go to "Server > IP addresses management" and click on the IP then associate the certificate with the IP.

Note 1:
I recommend using ssl.domain.com (that's what Google is using, short & sweet) OR secure.domain.com because many people have used domain.com or www.domain.com when filling out for the Certificate Request this could cause problems if your visitors type the address differently which will lead to a certificate warning.

Note 2:
I admit that there are different kinds of SSL certificates. If you buy a wild-card certificate you don't have to worry about any certificate warnings ... however it will not be a cheap solution.