The default config files that come with Asterisk and AsteriskNOW tell me everything and nothing at the same time. I would suggest AsteriskNOW using configuration files that are stripped of most of the comments and commented out options and only represent what is actually being used in the current configuration. This would make it easier to identify what has been created via the GUI and make manual editing (at least for me) much easier.
The default conf-set could always be provided in a separate folder as part of the documentation.
In addition to this I would suggest a kind of "expert mode" that allows editing the configuration through the web interface (like in trixbox).