If you have used cPanel to generate its own ssl certificate then this is what is called a 'Self Signed' certificate. It is Issued to and By your domain - which means that it is not a 'Trusted' certificate. For a certificate to be Trusted it has to be issued To your domain but issued By a Trusted Provider of ssl certificates - like Geotrust, GoDaddy etc.
You can use the cert you have created for testing a site, but you wouldn't want to use it for a live website. To use it you need simply to enable ssl in both of the configure.php files.
To get a Trusted ssl certificate then you need to take the code from the CSR to a Trusted Provider and use that to buy a certificate which you then Import to overwrite the self-signed certificate. After this either the Apache or Windows service needs to be restarted for the install to be completed.
Vger