Configuration management provides designers of automation systems with a framework to develop effective automation systems despite their inherent complexity. By managing the complexity of the system, and assisting in low-level decision-making, configuration management systems enable human designers, operators and system technicians to focus on high-level decision-making where their knowledge and experience are the most valuable. The development of flexible, modular small automation systems for the Advanced Recovery and Integrated Extraction System (ARIES) Pilot Line at Los Alamos National Laboratory, can serve as a case study for the development of a configuration management methodology. Furthermore, this case study can be used to identify potential design tools that can assist in the development of automation systems. An examination of a specific case, that of the Hot-side Electrodecontamination Chamber of the ARIES Pilot Line has been used to identify necessary research developments and demonstrate the utility of the configuration management process.