I had free signed SSL from WoSign and i found Opera complains about that certificate when accessing WHM.

So i wanted to set free Comodo signed SSL for my WHM hostname. This SSL will automatically renew for free and is recognized by 99%+ browsers.

This is what i did and what worked:
1) go to WHM / SSL Storage Manager and delete hostname related entries (keys and crts) there
2) go to WHM / Manage Service SSL Certificates and "Reset Certificate" for the: "Calendar, cPanel, WebDisk, Webmail, and WHM Services", then click "Apply Certificate to Another Service" and tick rest of the services to apply SSL on.
3) then in same section "Manage Service SSL Certificates" all services shoud have self-signed certificate.
4) i login the WHM server via SSH and execute: /usr/local/cpanel/bin/checkallsslcerts
5) as a result, it installed immediately cPanel certificate for the hostname and all the WHM services, i could see it in "Manage Service SSL Certificates".
6) When i Ctrl+F5 WHM webpage, i see it started using signed SSL and do not show any insecure warnings. Nice.

If you know better way, please kindly share.

Related topic: whm-cpanel-server-hostname-ip-redirects-wrong-web-site-internal-error-500-a/