The demand for natural resources (e.g., oil and gas, minerals, etc.), together with the high cost and operators fatigue associated with the classical teleoperation approach used by the offshore industry in Remotely Operated Vehicles (ROVs), brings the need for a higher degree of automation in the intervention tasks. To meet this requirement, the Underwater Vehicle-Manipulator Systems (UVMSs) are intended to be used in an autonomous way to perform Inspection, Maintenance and Repair (IMR) operations in the next fell years. Also, there is an increasing demand for alternative means of transportation in the underwater environment to assist in construction, deep-sea mining and general dexterous manipulation, which a single UVMS cannot perform. This work focuses on the motion control and coordination of UVMSs during cooperative transportation. Among the theoretical developments, the main contribution is the introduction of the Modular Control Methodology (MCM) for general multibody systems, whose potential engineering applications go beyond the class of problems that originally motivated this thesis. This novel methodology simplifies the control synthesis with a hierarchical approach, using standard controllers for the subsystems in the lowest levels of the control hierarchy and enforcing the constraints a posteriori. It also enables control allocation in the case of overactuation and optimal control synthesis. The MCM can also be used for coordination during cooperative transportation, since the prescribed formation can be treated as a set of constraints among the agents according to the established communication topology. The contributions made here are tested through numerical simulations in different scenarios.