Normally, an SSL certificate should be installed for the account user that owns the domain for which the certificate was generated.Any SSL installed onto the main shared IP will only be installed as the user nobody via WHM, so if you are using that main shared IP for an account, you'd first have to install as nobody in WHM, then go into root SSH and do the steps I had noted (Miraenda user is my non-staff account).
If you do not want to go through such a hassle, simply install a dedicated IP onto the account getting the SSL, then you can install the SSL using WHM onto the user's account rather than using the user nobody.
Change your main shared IP to something else from here:
WHM>>Basic cPanel & WHM Setup
Once the main shared IP has been changed, install the certificate. This method will allow you to install an SSL on an IP with multiple domains. Once done, you can change the main shared IP back to what it was. This method can only be used once. There is no recommended way to get multiple SSL certificates working on the same IP unless you make a custom virtual host entry in the pre_virtualhost_global file. This method is not cPanel recommended nor supported and they will not help you set this up.