The hybrid combination of hydrogen fuel cells (FCs) and batteries has emerged as a promising solution for efficient and eco-friendly power supply in maritime applications. Yet, ensuring high-quality and cost-effective energy supply presents challenges. Addressing these goals requires effective coordination among multiple FC stacks, batteries, and cold-ironing. Although there has been previous work focusing it, the unique maritime load characteristics, variable cruise plans, and diverse fuel cell system architectures introduce additional complexities and therefore worth to be further studied. Motivated by it, a two-layer energy management system (EMS) is presented in this paper to enhance shipping fuel efficiency. The first layer of the EMS, executed offline, optimizes day-ahead power generation plans based on the vessel's next-day cruises. To further enhance the EMS's effectiveness in dynamic real-time situations, the second layer, conducted online, dynamically adjusts power splitting decisions based on the output from the first layer and instantaneous load information. This dual-layer approach optimally exploits the maritime environment and the fuel cell features. The presented method provides valuable utility in the development of control strategies for hybrid powertrains, thereby enabling the optimization of power generation plans and dynamic adjustment of power splitting decisions in response to load variations. Through comprehensive case studies, the effectiveness of the proposed EMS is evaluated, thereby showcasing its ability to improve system performance, enhance fuel efficiency (potential fuel savings of up to 28%), and support sustainable maritime operations.