Assume your main domain is main.com which has document root /home/main/public_html
When you create an addon domain say addon.com, it will show the document root as
/public_html/addon.com (i.e /home/main/public_html/addon.com
That will make http://main.com/addon.com
accessible over http. So when you create an addon domain, make sure that the document root reads as:
/addon.com (i.e /home/main/addon.com). Even though this has nothing to do with SEO, it is always a good for better management of files.