In this paper, we introduce a basic multi-layered modeling framework for posing the problem of safe, robust and efficient design and control that may lend itself to ripping potential benefits from electrification. The proposed framework establishes dynamic relations between physical concepts such as stored energy, useful work, and wasted energy, on one hand; and modeling, simulation, and control of interactive modular complex dynamical systems, on the other. In particular, our recently introduced energy state-space modeling approach for electric energy systems is further interpreted using fundamental laws of physics in multi-physical systems, such as terrestrial energy-systems, aircrafts and ships. The interconnected systems are modeled as dynamically interacting modules. This approach is shown to be particularly well-suited for scalable optimization of large-scale complex systems. Instead of having to use simpler models, the proposed multi-layered modeling of system dynamics in energy space offers a promising basic method for modeling and controlling inter-dependencies across multi-physics subsystems for both ensuring feasible and near-optimal operation. It is illustrated how this approach can be used for understanding fundamental physical causes of inefficiencies created either at the component level or are a result of poor matching of their interactions.