The Controller Configuration entity is how you can configure a stock controller to have some different behavior for your instance of services. This largely involves:
You should never modify a stock controller configuration record. These stock records are used for Aptify's family of products and your changes may be overridden when you take maintenance. Instead you should create a record specific to your applications needs and add it to your service application.
As an example, lets say you want to allow anonymous access to the Space Threads controller for your service application. There is currently only one Controller Configuration record for the Space Threads controller. Here is its definition:
If you change this record to allow anonymous access, you will be allowing anonymous access to any other service applications using this configuration record. This is never what you want to do. Instead, you should create a new record and configure the controller according to your application's needs.