Ok, I understand the Title didn't make any sense so here I've tried to explain it in detail.

I'm using a hosting that gives me space for my domain and lets me "add on" other domains on it. So lets say I have a domain A, and I add on a domain B. Basically my hosting gives me a public_html where I can put stuff that shows when someone visits website A. But, when I add the domain B, it lets me put the content of B, INSIDE of that public_html so that website B.com can also be visited by going to A.com/siteB... Thats all good, except that Google has started indexing B.com as well as A.com/siteB, I'm ok with it indexing B.com, but I somehow want to prevent it from indexing A.com/siteB so that when people search for B, it doesn't end up showing A.com/siteB.

Any ideas? Let me know if the question is still unclear.