What is the Root Directory?
The Root Directory of the Master Domain (Primary Domain) on an account is the public_html/ directory. This is where you can publish files to be viewed online.
The root directory can sometimes also refer to / on the server. Normally with a shared server your will have access to everything in your users directory, which is located at /home/username/. If you connect with FTP using your cPanel username the files in that directory will be what you see as /. Therefore the root directory for your user may also refer to this directory.
A good simple explanation of how the Linux file system is organized can be found Here.
Addon Domains: You check your list of Addon Domains in cPanel > Addon Domains for the location/path for each Addon Domain or to set up a new Addon Domain