Here's one way to organize your files for Webware+Cheetah.
www/ # Web root directory.
site1.example.com/ # Site subdirectory.
apache/ # Web server document root (for non-servlets).
www/ # WebKit document root.
index.py # http://site1.example.com/
index.tmpl # Source for above.
servlet2.py # http://site1.example.com/servlet2
servlet2.tmpl # Source for above.
lib/ # Directory for helper classes.
Site.py # Site superclass ("#extends Site").
Site.tmpl # Source for above.
Logic.py # Logic class inherited by some template.
webkit.config # Configuration file (for WebwareExperimental).
Webware/ # Standard Webware's MakeAppWorkDir directory.
AppServer # Startup program (for standard Webware).
Configs/ # Configuration directory (for standard Webware).
Application.config
# Configuration file (for standard Webware).
site2.example.org/ # Another virtual host on this computer....