Seasonal storage is a key feature of future decarbonized energy systems with a high share of renewable energy integration. Power-to-Gas technologies represent a promising solution to enable such storage. They allow the conversion of surplus renewable electricity into e-fuels and their storage in the long-term. Their utilization enables the integration of the electrical, fuel and heating sectors, by converting electricity into fuels and recovering the waste heat from the process. Nevertheless, to design the most profitable management strategy for such systems, advanced control tools are required. This study introduces a novel control architecture for multiple multi-energy systems that share an e-fuel seasonal storage. Each energy system has its own short-term control logic, based on Model-Predictive Control (MPC), which manages day-ahead energy exchanges, while a long-term MPC controller considers yearly dynamics and the system as a whole. This gives additional constraints to the short-term controllers, which ensure the fulfillment of yearly goals. A multi-temporal and multi-spatial hierarchical control architecture is proposed, which enables optimal seasonal storage management, and its operation is verified in a Model-in-the-Loop configuration. The controller efficiently uses seasonal storage to balance seasonal mismatch between production and demand, resulting in higher utilization of renewable energy, lower emissions and costs.