U-CAT is a highly maneuverable biomimetic four-fin underwater robot for operating in confined spaces. Because of its novel mechanical design and specialized purpose, the traditional autonomous underwater robot control methods are not directly applicable on U-CAT. This paper proposes a novel modular control architecture that can be adopted for different application scenarios. Within this framework, we implement and test several 2-degree-of-freedom (DOF) controllers and discuss the test results. Furthermore , we describe and implement an actuation coupling method by prioritizing the selection of DOF with fuzzy membership functions and demonstrate the approach for 3-DOF control. The results show that the proposed DOF prioritization approach helps us to improve tracking both in the case of human in the loop and automatic control. Finally, we describe long-duration field experiments in realistic environmental conditions.