You need to configure the nameservers of the domain you already own to the nameservers of the primary domain name. This has to be configured on your account in order to use it. You have two options:
1) To park it over your primary domain so that it opens your main site.
To access the Parked Domains feature, click on the corresponding icon located on the main screen of your cPanel interface.
To add a parked domain, enter the name of the domain in the blank field and click on Add Domain. (Make sure to register the parked domain with a valid domain registrar and set the nameservers properly or else it will not work)
2) To create a new site with your new domain using Addon Domain.
Through the Addon Domains feature you can add additional domains to your account. An addon domain allows you to reach a domain when entering the name of the addon domain into a browser. This means that you can host additional domains in your account.
To access the Addon Domains tool, click on the corresponding icon located on the main screen of your cPanel interface. Enter the name of the addon domain in the blank field next to New Domain Name. Enter the name of the directory which contains the subdomain that the addon domain will point to in the blank field next to Subdomain/FTP Username: (This directory will be the location for the addon domain's files, just as public_html is the location for your primary domain's files.). Type in the password for the new addon domain, and click on Add Domain!