How to deal with addons domains ?

Hi,
He realized I had a problem with my domains hosting.
I have a main domain for the hosting and several "addons" domains on it and the problem is that you can access to my sites through differents paths like:
addondomain (the normal way)
and
maindomain/sitefolder (the wrong way)

So Google is ranking at least twice my content, and that's why I would like to fix that.
I hope I explained clearly if you know how to fix that would be great, thank you

You'll need to contact your web hosting company and likely log a support ticket regarding changing your root directory. I didn't have permission to do this myself anyways.

You'll want your primary domain's contents copied to a new desired sub-folder, just as your add-ons are in different ones.

Once it's confirmed that all your domains are functional, you can then remove the http://www.maindomain/subfolder(s) urls using webmaster tools, or let them 404 and produce crawling errors until they're de-indexed.

You can delete the original domain's contents\folders (being careful not to delete any "domain" subfolders).

You likely already did the www redirect with .htaccess to prevent duplicate content\listings, so this is a good measure to take as well.