cPanel will automatically generate a free hostname certificate during nightly maintenance as long as the hostname resolves to the Main IP address of the server. However, you're welcome to use the following procedure to manually generate the certificate if you need it sooner.
If you need to replace a third-party certificate with a free hostname certificate, you can remove the third party certificate with the following steps:
In order to install the free hostname certificate use the following steps:
/usr/local/cpanel/bin/checkallsslcerts
Documentation: The checkallsslcerts Script