Over the years, electronic design automation (EDA) has been moving up the design abstraction ladder. Starting from automating tasks like placement, floor-planning and routing in integrated circuits design, EDA now encompasses many system-level design tasks. However, the next challenge facing the EDA community is to develop methods and also tools for cyber-physical systems (CPS) design. For these systems, physical processes, control algorithms that control these processes, and the computation and communication platforms on which these control algorithms are implemented — are all modeled and designed in a tightly integrated fashion. Currently available EDA methods and tools are not equipped to handle such integrated modeling and design. In particular, there is a big disconnect between modeling tools — like Matlab/Simulink — that are used for modeling plant dynamics and designing their controllers, and the tools that are used to design and configure the hardware/software platforms on which these controllers are eventually implemented. In this extended abstract we discuss the consequences of this disconnect and possible ways of addressing this situation.