This paper presents development experience of architecture, principles of functioning, software engineering and modeling of multi-agent system for information support of regional business processes. The main purpose of the system is integration of distributed heterogeneous information resources and web-services devoted to innovations in the Internet. The system provides an automated search of potential business partners, an interactive innovation chains construction and selection thae most efficient of them. The necessity of system dynamics modeling methodology using in development of business processes support systems is discussed. Agent-based technologies are examined. Special attention is given to development of virtual business environment conceptual model. Our conceptual model is used as a basis for the system structure, algorithms, functionality and relationships between its main architectural components representation. Specifically, we show how to use the conceptual modeling methodology, system dynamics and multi-agent system technology in developing a multi-agent system for integration of distributed heterogeneous information resources and services devoted to innovations.