I assume you added another domain as an addon domain. I wouldn't worry about how it shows up under the subdomains in your control panel. I thought the same thing to when I first signed up with vodahost with my primary domain. When you add an addon domain a folder will be created in your ftp. So when you go to publish a page for your add on, just make sure the folder is: public_html/youraddondomainname.
As an example, my primary is journeysadmin.com. Under that primary, I host many other addon domains, one being journeyshappen.com. When I added journeyshappen.com, it created a subdirectory of the same name. So when I publish I publish to the folder: public_html/journeyshappen.
If you access
www.journeyshappen.com, you will see that the primary name (journeysadmin.com) is no where to be seen.
I hope that this answered your question.