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This paper addresses the problem of modeling and simulating large set of heterogeneous networked embedded systems which cooperate to build cost-efficient, reliable, secure and scalable applications. The purpose of this task is an application-driven top-down design flow which starts from application requirements and then progressively decides the general architecture of the system and the type and structure of its HW, SW and network components. In the past, a considerable research effort has been done to create specific tools for each design domain ---software, hardware and network---, and to integrate them for data exchange between models and their joint simulation. However, the advantages and drawbacks of different combinations of tools in the various stages of the design flow have not been discussed. The paper describes and discusses how to combine different modeling tools to provide different modeling and simulation alternatives for the design of networked embedded systems devoted to complex distributed applications. The problem is faced both theoretically and practically with a real application derived from a European project.