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.  :)