This paper addresses the problem of designing guidance, control and navigation systems for autonomous underwater vehicles (AUVs). Its contribution is twofold: i) it introduces a new methodology for the integrated design of guidance and control, and ii) it describes a novel approach to the analysis and design of multi-rate complementary filters for navigation. The methodologies proposed lead to an efficient procedure for the design of controllers for AUVs, to accurately track reference trajectories defined in an inertial reference frame. The paper illustrates the application of that procedure to the design of a tracking controller for the MARIUS AUV. The design phase is summarized, and the performance of the resulting controller is assessed in simulations, using dynamic models of the vehicle and its sensor suite.