The design of resilient infrastructure is a critical engineering challenge for the smooth functioning of society. These networks are best described as cyber-physical systems of systems (CPSoS): integration of independent constituent systems, connected by physical and cyber interactions, to achieve novel capabilities. Bioinspired design, using a framework called the ecological network analysis (ENA), has been shown to be a promising solution for improving the resilience of engineering networks. However, the existing ENA framework can only account for one type of flow in a network. Thus, it is not yet applicable for the evaluation of CPSoS. This article addresses this limitation by proposing a novel multigraph model of CPSoS, along with guidelines and modified metrics that enable ENA evaluation of the overall (cyber and physical) network organization of the CPSoS. The application of the extended framework is demonstrated using an energy infrastructure case study. This research lays the critical groundwork for investigating the design of resilient CPSoS using biological ecosystems inspiration.