I just created an addon domain on cpanel and I see a subdomainwas also created for the main domain, eq: I had: maindomain.com and I added seconddomain.net and I have seconddomain.maindomain.com too. That means that if I create a blog on seconddomain.net, google will start to rank seconddomain.maindomain.com too?
Well not if you provide its url to Google, or link it. Your second domain should work fine with url seconddomain.net. So just use that url to submit it to google. Similarly link it with your main url ie seconddomain.net from the href.
You can also create a redirect - redirect the sub-domain to the seconddomain.net just to insure it can't be reached the way you don't want it to.