> > Is there a way to alias www => www.intranetsite.com to 
> help 
> > standardize the links and directory tree and avoid 
> > duplicates?
If you aren't concerned about the structure of the mirror, you could have a
look at using a non-default "Site Structure" (Options > Build), maybe
something like "Html in web/, images/other in web/images/"

That should keep everything collected together.