An add on domain allows you to run a separate web site to your primary domain.  All Basic and Business plan accounts come with unlimited add on domains at signup.  When you setup an add on domain it makes a folder in your public_html folder and you upload the site content into that folder.  Essentially you are then running 2 separate sites, separate content, off one account.

An "add-on" site must have its own URL (domain name), which must be purchased from any registrar you wish. If you already have purchased a domain name that is parked or otherwise not pointing to a site, you can use that. It would appear to the world to be a completely unrelated, separate site.

From the nature of your questions, you sound extremely confused. Perhaps you could recount what you have, and what you've purchased, and what you want to end up with?