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The Document Root essentially acts the same way public_html does for the main account, but for the newly created addon domain. As a reminder, this is where your new (addon) site's index page and other site files belong.
You can also create a new ftp FTP account for the addon site. This is generally used if you want to restrict access to your primary site by only allowing access to this folder and those below it. To do this, check the box next to "Create an FTP account associated with this Addon Domain" and follow the onscreen information.
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