The default file for any web directory is index.html. That means when visitors access http://www.yourdomain.com, the server really sends them to http://www.yourdomain.com/index.html. This works for any publicly accessible directory on your system, including subdomains. For instance, if you typed http://www.yourdomain.com/links/ in your browser, you would view the index.html file in the /links/ directory.
When uploading a main web page for each directory remember to name it index.html. Advanced users may utilize PHP files, shtml files, etc. If your web site is not based in html, then make sure your main files are renamed index.extension (for example, index.php, index.shtml, index.asp, etc.).