Your main domain is the one associated with your hosting account and generally, the files for that site go in the root of the account, which is usually public_html.
If you want to install another site on your hosting account, WP or otherwise, it goes into it’s own folder off the root. For example, if you want to install WP, create a folder in the root of the account called wordpress
and have your hosting account’s auto installer install it there, specifying /wordpress
as the location.
But, before you can use an “Addon Domain”, you actually have to have a domain to use; that is, you have to buy one somewhere. And if you do not buy it through your host and have it associated with your hosting account, then you have to change the nameservers of that domain, where you purchased it, to the nameservers of your hosting account. It can take up to 48 hours for this change to become effective.
To sum up:
– if your current “main domain” is myfirstsite.com
and you want to add mysecondsite.com
to your hosting account, you have to purchase mysecondsite.com
from somewhere.