Marine energy systems are rapidly evolving, following the demand for decarbonization and increased energy efficiency. Design options are ever expanding due to an increased degree of electrification, inclusion of energy storage systems, novel energy converters such as fuel cells and dual- fuel engines, and alternative fuels such as hydrogen, methanol, or ammonia. These increasingly complex layouts also necessitate the development of accompanying energy management systems to orchestrate the operation and power split between different sources in an optimal fashion. Design of such systems is increasingly supported by simulation and optimization methods. Optimization criteria can vary depending on the intended vessel mission and most frequently include metrics such as; energy efficiency/range optimization, OPEX/CAPEX minimization, system health, and uptime considerations. The need for these methods is further emphasized by the characteristics of new energy converters and storage systems, considering the in-use degradation of battery and fuel cell systems, increased footprint required to place these systems, (early adopter) cost, and the reduced energy content of alternative fuels. In the current paper a methodology is explored for co-design of the energy system together with the energy management in an integrated and optimal fashion. The testcase considered is that of a fast ferry operating on H2 powered by a PEM fuel cell. The benefits are compared with traditional design approaches, in which either the system layout or energy management logic is optimized, in order to quantify the added benefit of integrated design. While the testcase for this methodology is a commercial vessel, the methodology is designed to be generally applicable and may also strongly benefit the design of complex naval vessels. While it is unlikely that naval vessels will adopt hydrogen as a primary fuel, it can become a part of the energy sources onboard to supply smaller (unmanned) assets (UXVs) or to run fuel cells in support of low-signature operation. Using co-design to optimize towards metrics such as footprint or system health is vital to integrate these novel energy systems and guarantee their effectiveness in future marine powertrains.