Where to Upload Files for an Addon Domain
Each Addon Domain is assigned to a directory on your account. This directory is typically a subdirectory in your public_html.
Uploading Your Site
After you have assigned an Addon Domain via the Bluehost domain manager, there will be a sub-folder created in your public_html folder (e.g. "/public_html/addon_domain_foldername"). You will need to upload the files for this Addon Domain to the subfolder created.
You can also refer to this article: FTP - Uploading the website for additional information.