By default, addon domains and subdomains use folders beneath the public_html folder. So the root directory for an addon domain named yourdomain.com would by default will be public_html/yourdomain.com.
To change the document root folder follow the below steps:
Step 1: Log into the cPanel. In the "Domains" section, click the Addon Domains or Subdomains icon, depending on which you'd like to modify.
Step 2: In the Modify a Domain section at the bottom of the page, click the icon next to the current document root for the domain you wish to modify.
Step 3: In the popup window, enter the new document root and click Change.