You have to upload the files for an addon domain to its webroot directory.
When creating a new addon domain you are asked to specify its webroot directory. If you are not certain which it is please log in your Cpanel and go the Addon domains section. Next to each addon domain you will find which its webroot is.
Also when uploading files through Cpanel's file manager, you will be asked which directory to go to first. There you can choose directly the addon's web root.
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