> First of all I would prefer to rename:
> /home/mywebsites/foo/www.foo.com/catalogengineering.html

Set Options / MIME types
php3 <-> text/html

> How can I give this option in WinHTTrack? I couldn't find 
> it in the options tabs.

Set Options / Build structure / Options

> And how does it work exactly?
in the user-defined structure:
%h%p/%n%[page].%t

> Otherwise how to do it in the command line version?
-N "%h%p/%n%[page].%t"