Off the wall - sub-domain question

I have a main domain (of course) and a sub domain. I'm really trying to steer my personal stuff away from the main one and have focused all of my php development to the sub-domain. Lately I noticed that google catalogs my sub-domain site stuff under the main domain name and the links that come up lead to that domain name with the path that takes the user to the sub-domain's home folder and beyond. Is there something that php (apache??) can do to control either google's robots or the user's view (url) so that it appears as a page of my sub-domain? I'm really new at this stuff and know nothing. I'm lucky that google is even finding my site! IN advance - I apologize for this off-topic question, but this place is a source of much knowledge, so I just threw in a quick interlude here to pick someone's brain. :)