The paper reports a tool which was originally developed to assist managers to easily visualise, analyse and manage complex innovation systems. Strategy management literature appears to be somehow functionally myopic (Hines et al, 2006). A gap is common between ambitious strategies and operational-level processes. For this purpose, as a bridge, the tool gives holistic (as-is and should-be) views of the essential activities conducted by the main actors, across-functions and across-organisations, to effectively and sustainably complete every innovation process in alignment with the strategies. Since these main actors form a complex system per-se, the tool is useful to analyse and manage their strategic activities prior to defining the operational-level activities of the other (subaltern) actors committed to specific process. The first analysed companies reported 7 m value-added from the project. Since then, the Premium Automotive Research Centre and the National Skills Academy for Manufacturing have taken over the tool to implement it in other manufacturing companies. Meanwhile the Warwick Innovative Manufacturing Research Centre and the National Health Service have also been adapting and using the tool, combined with other manufacturing tools, to analyse and manage complex systems in healthcare organisations. The paper illustrate the lessons learned through some case studies.