This article covers generating a CSR that will cover a domain for use with a 3rd-party SSL in both cPanel and WHM.
1) Log into your cPanel or WHM and navigate to the following location:
Security > SSL/TLS > Generate, view, or delete SSL certificate signing requests
SSL/TLS > Generate an SSL Certificate and Signing Request
2) In the "Domains" section, add your domain.
3) Fill out all other required fields appropriately and click the Generate/Create button.
Once done, the resulting CSR can be provided to a Certificate Authority. After they have issued the SSL, it can be installed in the following locations of your cPanel and WHM.
Security > SSL/TLS > Manage SSL sites
SSL/TLS > Install an SSL Certificate on a Domain