This work introduces two multi-level control strategies to address the problem of guidance and control of underwater vehicles. An outer-loop path-following algorithm and an outer-loop trajectory tracking algorithm are presented. Both outer-loop algorithms provide reference commands that enable the generic submarine to adhere to a three-dimensional path, and both use an inner-loop adaptive controller to determine the required actuation commands. Further, a reduced order model of a generic submarine is presented. Computational fluid dynamics (CFD) results are used to create and validate a model that includes depth dependence and the effect of waves on the craft. %The model and the procedure to obtain its coefficients are discussed, and examples of the data used to obtain the model coefficients are presented. An example of operation following a complex path is presented and Results from the reduced order model for each control strategy are compared.