This technology pertains to the use of a system to balance the multiple levels and compartments within a large ship that includes compartments at multiple levels that have optional stages of flooding, partial flooding, machine flooding, and/or variable buoyancy. This system pertains to managing all of the compartments as a whole, in addition to each level on the ship, to ensure that the ship is balanced on the water, and to ensure that the ship is at the correct level in the water, such as adjusting the buoyancy when there is additional weight on the ship, including additional equipment, additional resource processing and storage, and other characteristics that would change the levels such as the flooding of compartments to release submarines and other types of aquatic equipment from the large ship.