Two domains, one hosting service

I have my main domain, site1.com (where most of my various sub-sites are), and I also have site2.com.

I only have one hosting service at the moment. site2.com just points to site1.com/site2/

Right now /site2/ is empty, but if I go to site2.com it still shows a PR.

I am going to start using site2.com again. It will be a completely different subject than site1.com.

My question is, do I have anything to worry about? Will Google (or other engines) see site2.com but also see site1.com/site2/ and think it is duplicate content?

I know that I should never link it like this - site1.com/site2/. I will always use site2.com, but people have said that if you even view a page, the google toolbar can give the site info to google. I have viewed site1.com/site2/ in the past. Will this be a problem when I start using site2.com again? Will they truely be seen as two different domains? Or will I have problems?

Any suggestions/thoughts are very much appreciated!