Self-organizing Systems exhibit numerous advantages such as robustness, adaptivity and scalability, and thus provide a solution for the increasing complexity we face within technical systems. While they are attractive solutions, due to their nature, designing self-organizing systems is not a straightforward task. Artificial evolution has been proposed as a possible way to build self-organizing systems, but there are still many open questions on how an engineer should apply this method for this purpose. In this paper we propose a design methodology for evolving self-organizing systems, that marks the major cornerstones and decisions the designer has to face, thus providing a practical set of guidelines.