Techniques are described for implementing automated control systems that manipulate operations of specified target systems, such as by modifying or otherwise manipulating inputs or other control elements of the target system that affect its operation (e.g., affect output of the target system). An automated control system may in some situations have a distributed architecture with multiple decision modules that each controls a portion of a target system, and may further have one or more components that interacts with one or more users to obtain a description of the target system, including restrictions related to the various elements of the target system, and one or more goals to be achieved during control of the target system. The component(s) then perform various automated actions to generate, test and deploy one or more executable decision modules to use in performing the control of the target system based on the user-specified information.