Seeking Opinions about PHP Directory Organization and Permissions on Linux

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Howdy all,

I have been using PHP, MySQL and Apache on Win2K for about a year now and 
have recently begun the process of switching development to Linux -- 
RH9.0.
Yesterday (by using the excellent reference by Patrick Harper, 
http://www.internetsecurityguru.com/documents/snort_acid_rh9.pdf ) I 
finally successfully installed from source MySQL-4.0.16, PHP-4.3.4, and 
Apache-2.0.48 on Linux, and a test phpinfo() page worked as expected. 

Now I need to migrate several multi-file (db_connect files, function 
include files, C executables) apps from windows to linux, so I was 
wondering:

1.  How *nix users organize their 'include' and 'session' directories 
(e.g., outside the web root? how deep in the directory structure?).
2.  Whether all files (including C executables) should be owned by root, 
and what permissions should be set. For example, I was logged in as root 
when I made
     the phpinfo() file, so it  _is_ owned by root. Permissions were set 
automatically to 0644. Is this customary? And who/what will own the 
session files as they are created?
 
Perhaps I'm over-thinking these issues, but I've not much experience on 
*nix compared to windows, and it's Friday afternoon in my spot of the 
world. 

Thanks in advance for any suggestions / tips, etc... 

 dave

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