Trying To Set Up A SSL Certificate On My Dedicated Server

getting my SSL certificate loaded properly onto my dedicated server.

The initial problem was with when I tried to log in via WHM or cPanel, I got this notice displayed on the page:

There is a problem with this website's security certificate.
The security certificate presented by this website was not issued by a trusted certificate authority.

The security certificate presented by this website was issued for a different website's address.

Security certificate problems may indicate an attempt to fool you or intercept any data you send to the server.

We recommend that you close this webpage and do not continue to this website.
Click here to close this webpage.
Continue to this website (not recommended).”

I figured that to get rid of the notice displayed, then I would need a SSL certificate, so I bought one from Trustwave.
Everything went okay with the initial download and things were running smooth until I got to installing the intermediate certificate but I just can't find
where the installation instructions say to place the certificate.

Downloading the certificates isn't the problem. It is the instructions (see below) which were copied from Trustwave’s own “sslcertificates/install” link which tell me what to do, all okay, just I can't find where to install the intermediate certificate in WHM!

Instructions given by Trustwave are -
"Save the xroot.crt file to a directory on your server, and be sure to note
the directory path. Generally, you can find Apache's configuration file in
/etc/httpd/conf/httpd.conf, but you may need to search for it. Sometimes the SSL configurations are in a file called ssl.conf.

Open the configuration file in a text editor and search for the virtual
host. You can search by your server's address or IP address. Once you find the virtual host which matches your host, look for two lines that start with SSLCertificateFile and SSLCertificateKeyFile. Add (or adjust) a line right below those two that shouldread: SSLCACertificateFile /path/xroot.crt
Save and close the configuration file."

I don't know where to find places such as "Apache's configuration file in
/etc/httpd/conf/httpd.conf" and "ssl.conf" - in WHM/cPanel does anybody know where these places are? And I have just noticed that I'm back to getting the "untrusted website stuff" displayed when I try to log onto either cpanel or WHM in my server.