You should basically edit the configuration file manually, however I configured it so that the raw configuration file was split into different include files, each of which is configured in my version control system. Then I created a project for configuration, and then for the whole configuration. Therefore, when something changes in the configuration, CC.NET itself pulls out the changes, recreates its configuration files and updates the system configuration.
This means that anyone can edit the configuration (if they can access files in sourcecontrol), and no one should go into the program files directory of the CC.NET machine itself.
Not sure if this question answers your question, but this is how our installation works.
Mmarquee
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