I am unsure what to exactly put in here on windows server 2008 when creating the CSR file.
My wesbite is example.com. with the other links in the form of:
example.com/index.php/example
So what would i put as the common name to ensure the entire site has a SSL certificate?
HTML pages and directories are irrelevant. The common name would be example.com. CN=example.com. You probably also want Subject Alternative Name (SAN) to be DNS Name=www.example.com if your users may access your website by either example.com or www.example.com. If you have a lot of hostnames, you may require a "wildcard" certificate, where *.example.com shows up in the Subject Alternative Name list, and that will cover every hostname under example.com... such as www.example.com, ftp.example.com, mail.example.com, etc... but only one level deep, so a wildcard would not cover sub.www.example.com, for example. Wildcard certs are usually more expensive and often frowned upon as they are generally seen as less secure. If the subject (common name) on the certificate were example.com, that will cover all the files and directories hosted on example.com, such as http://example.com/welcome.php, http://example.com/users/newuser.aspx, etc.
You just have to consider your domain name as the Common Name for your certificate.
In your case : CN=example.com
Certificate CN does not take care about subdirectories for the domain.
index.php/example are just subdirectories from your main domain example.com.
The certificate will not take care about them.
However, certificate will take care about subdomains like aa.example.com or bb.example.com. In this case you will have to add a SAN for each, or at very least, a wildcard certificate : *.example.com.
