As you set up your Addon domain, the system will create a folder for you. By default, the folder name will be as it is of your addon domain, without the "www." For example, if you add a domain called www.addondomain.com , there will be the folder called addondomain.com Upload your files to this folder.
You can upload files to an addon domain using your current account or FTP, You can set up a new one to manage your Addon domain files.
More details on FTP settings: http://www.reprisehosting.com/client/knowledgebase.php?action=displayarticle&id=3