The engineering of large-scale cyber-physical systems (CPS) increasingly relies on principles from self-organisation and collective computing, enabling these systems to cooperate and adapt in dynamic environments. CPS engineering also often leverages digital twins that provide synchronised logical counterparts of physical entities. In contrast, sensor networks rely on the different but related concept of virtual device that provides an abstraction of a group of sensors. In this work, we study how such concepts can contribute to the engineering of self-organising CPSs. To that end, we analyse the concepts and devise modelling constructs, distinguishing between identity correspondence and execution relationships. Based on this analysis, we then contribute to the novel concept of “collective digital twin” (CDT) that captures the logical counterpart of a collection of physical devices. A CDT can also be “augmented” with purely virtual devices, which may be exploited to steer the self-organisation process of the CDT and its physical counterpart. We underpin the novel concept with experiments in the context of the pulverisation framework of aggregate computing, showing how augmented CDTs provide a holistic, modular, and cyber-physically integrated system view that can foster the engineering of self-organising CPSs.