Firstly when your issuance email arrives you will have two certificates in the email - your server certificate and a chained root certificate.

Copy the chained root certificate into a text editor such as notepad and save as chain.crt.
Copy your web server certificate into a text editor such as notepad and save as yourdomain.txt.

CPANEL

It is rare that cPanel customers will have direct access to install SSL certificates. If you are a hosting customer and you use cPanel, check with your hosting provider how you would go about installing a CSR

WHM (Web Hosting Manager)

WebHost Manager is the control center of the CPanel / WebHost Manager package. It is used to set up and manage accounts. Use WHM to install your issued certificate.

Once you have generated or received an SSL certificate (refer to Generating an SSL certificate for more information), you can install the certificate using WebHost Manager. You need both the certificate and key files to install the certificate.

Step 1: To install an SSL certificate:

Click on the Install an SSL Certificate and Setup the Domain link in the SSL/TLS menu.

Enter the domain, user name, and IP address for the certificate in the Domain, User, and IP Address fields.

Click on the button to paste the .key and .crt files for the domain into the available display spaces, if they are currently on your server. Otherwise, copy and paste the .key and .crt files into the available display areas.
Note: If you generated the certificate using WebHost Manager, the certificate files will be available .

Replace the existing .crt file with yourdomain.txt (as emailed by RapidSSL.com)

Copy and paste the chain.txt chained certificate into the available ca-bundle display area