How to engineer agent-based system is essential factor to develop agent or agent-based system. Existing methodologies for agent-based system development focus on the development phases and activities in each phase and don’t enough consider system organization and performance aspects. It is important to provide designer with detailed guidance about how agent-based system can be organized and specified. This paper defines computing environment in view of domain, proposes the methods that identify domain, deploy agent, organize system, and analyzes characteristics of the established system organization.