When you upload your web pages, it is important that you upload them to the correct location.
The directory in which your pages should be stored is either the 'www' folder or the 'public _html' folder. These folders are the same and contain the same files.
If you are uploading files to a subdirectory. You will notice that inside the 'www' or 'public _html' is a folder with the same name as your sub domain. This folder is the root directory for your subdomain and therefore any files for that particular sub domain should be located here.