Make sure that you have put your website files in the domain directory, which is a subdirectory of your username directory:
/home/username/yourdomain.com/your files go here
As far as your HTML class is concerned, I recommend creating a subdomain. You can do this in the control panel (same as adding a domain), and go for something like class.yourdomain.com. That will keep your HTML class files completely separate from your website (it will create a separate subdirectory in your username directory).
-- si-blog --
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