In this paper, a sub-region tracking control scheme is proposed for an Underwater Vehicle-Manipulator System (UVMS). In the proposed controller, the desired primary task of the UVMS is specified as two sub-regions that are assigned for the vehicle and end-effector. The unit quaternion representation is utilized to achieve singularity-free attitude tracking control. In addition, due to the kinematically redundant system, the controller also enables the use of self motion of the system to perform sub-tasks (drag minimization, obstacle avoidance, manipulability and avoidance of mechanical joint limits). Despite the parametric uncertainty associated with the underwater dynamic model, the controller ensures the sub-task tracking without affecting the sub-region and attitude tracking control objective. The controller has been designed based on a Lyapunov type approach. Results from simulations are presented to demonstrate the benefits of the proposed control law.