Why are there so many darn directorys??
There is one directory per configuration file, and there are a lot of configuration files in the system.
How does one know the order in which they copied the original /etc directory?
The template fragments in the directories are processed in asciibetical order. Only the configuration files related to the event in question are processed.
In 7.0alpha it's driven by a directory tree in 'templates2expand'. For previous releases, you need to check the various action scripts in the relevant event directory.