not that i know of, i had the same question awhile back and i was told it was just the way it was...  im assuming you talking about when you choose copy link from the file manager area, what i do is i  manually change it once you post it to your code or whereever, 

 i have not yet seen a solution or option to change how it links to it

A primary domain has its root (/) in /home/ACCOUNT/public_html/
A subdomain or add-on domain has its root (/) in /home/ACCOUNT/public_html/dirname/

If a server is set up correctly, you should see the subdomain or add-on domain name in the browser address bar. Otherwise, you are likely to see http://www.primarydomain.com/dirname/ in the browser. That can be easily fixed with URL rewriting in your .htaccess file.

When you say that your "images" have the "bad" form of the address, where are you seeing this address displayed? It's not clear to me from your question just where you are seeing this address. In normal operation of a page, the user doesn't see the image address, and if you are using an image as a link, it should show whatever address you gave in the <a href=. Do you have a relative address in the link, and it's prepending the "bad" form of the site address rather than the "good" form? That's all I can guess. If so, you would be seeing the "bad" address in the browser's address bar, and URL rewriting would fix both.

As Mr.Phil noted this may be .htaccess related. By any chance do you have hotlink protection enabled, or an existing .htaccess file with rules that may be causing this?

Well, to answer your original question, you'd need to manually change the link that the file manager gives you since there's no configuration option to change it automatically. For example, if you see the links as http://www.primary.com/addon/image.jpg, just change it do be http://www.addon.com/image.jpg.