The paper presents the methodology how to implement model-driven software configuration process in projects of developing applied computer systems and software. A methodology consists few dependent blocks that together allows decrease manual works of implementation and support configuration management process. The most important blocks of the methodology are problems and actions monitoring systems in project and database of knowledge. Monitoring systems can fix all problems in project. Knowledge database consist many rules. Using forward chaining procedure become possible to generate new rules in knowledge database that helps determine is some problems depends on configuration management area and find solution of this problem. New rules generation process help to make corrections in configuration management model. Configuration management model presents all actions and relations needed for implementation of configuration process. Monitoring systems and knowledge database can change current model according to changes in project. The paper describes also risks and limitations of using this methodology and necessary researches to make this methodology useable in projects