Many of the folders in the root you just need to ignore, as your cPanel uses them to provide many of the features (such as Email, Ruby, Password-Protection, etc.). The only folder that you may use is the public_html folder. The contents of this folder is visible to the world wide web, and can be accessed directly from your website.
Inside your public_html, the vti_ and _private folders (etc) are related to FrontPage Extensions, which HelioHost offers to it's customers. If you are not planning on using FrontPage Extensions, then you can disable them within your cPanel, which will also delete these folders.
The cgi-bin folder inside your public_html is essential for creating scripts in many languages. Best don't delete this.