Use the site.conf and localOverrides.conf files to make modifications.  

site.conf contains global variables which are required for basic configuration.
defaults.config contains initial settings for many customizable options in WeBWorK.  Do not edit defaults.config!  It will be overridden next time you upgrade.

The localOverrides.conf file is read after the defaults.config file is processed and will overwrite configurations in defaults.config.  Use this file to make changes to the settings in defaults.config, as it will be left alone when you upgrade.

This new  configuration system should greatly simplify the process of 
updating webwork2 since it is less likely
that one will need to modify the config files when upgrading.  Default configurations or permissions for 
new features will be defined in defaults.config and will allow automatic upgrades.  You can override these at any point from localOverrides.conf.

FIRST TIME RECONFIGURATION

COPY site.conf.dist to site.conf.
COPY localOverrides.conf.dist to localOverrides.conf.

MODIFY site.conf using the data from your global.conf file for the entries contained within site.conf.  
In particular you will need to fill in the server name, the 
password for the database and any modifications you have made as to the 
locations of various directories.

UPDATE localOverrides.conf to reflect any local customizations that you had made to global.conf.