Uh... I'm not sure I understand your question. Scratch that... I KNOW I don't understand your question.
What do you mean tell Apache where the PHP files are? I know that you can set the doc_root in PHP's config file...
; The root of the PHP pages, used only if nonempty.
; if PHP was not compiled with FORCE_REDIRECT, you SHOULD set doc_root
; if you are running php as a CGI under any web server (other than IIS)
; see documentation for security issues. The alternate is to use the
; cgi.force_redirect configuration below
doc_root =[code]
Is this what you were looking for?