Does Addon domain affect SEO

Question

 i have a main domain and an addon domains. Both have separate websites. Consider main.com is my main domain and addon.com is my addon domain name which is pointed to a sub directory called "addon".

I can access addon.com by using the following 3 ways.

addon.com
main.com/addon
addon.main.com

Are these urls are indexed separately by search engines? If so how can i prevent this?

Does Search engine think main.com/addon as a page in the main.com?