Currently, the system works this way: The default config "config.ini" holds all data which is necessary for the pack.
!!!DO NOT EDIT THIS FILE!!!

Now, you can create your own user_config.ini and add the necessary data to the sections like in config.ini.
The values of user_config.ini overrides the one in config.ini.

Example: When you want to increase e.g. the ZPM's maximum capacity, add the following to a blank file and call it user_config.ini:

# Starting the file...
# Anything which starts with a sharp is a comment and won't get recognized!

[zpm]
# We are changing the capacity! Horray for lifesupport cheating!
capacity = 10000000

# End of the file

Note: Every parameter is explained in config.ini!