The maritime industry is undergoing a significant shift towards more sustainable and efficient forms of transportation. As a result, designing Power, Propulsion and Energy (PPE) Systems for future vessels presents new challenges that require a systematic approach that reduces the risk in development and implementation. This paper focuses on three aspects of such a systematic approach: Model-Based System Engineering (MBSE), Co-design, and Verification and Validation. The MBSE approach can be used to mitigate the risks associated with the transition by maintaining a clear traceability of user needs, functional requirements and physical realizations. A rigorous needs analysis and functional design reduces the optimisation design space that results in a significant reduction in the complexity of a design optimisation problem. Further, co-design is discussed as a methodology for a combined optimisation of the hardware and software design where the Modular Energy Management approach supports automated controller generation for the optimisation, a key challenge when optimising PPE systems. An important aspect of the MBSE approach is the use of models for the verification and validation of the developed designs. However, the successful use of models is contingent on their applicability. This paper proposes a way to categorise model confidence for verification and validation studies.