A new approach for propulsion system layout that increases power and enhances the efficiency of submarine propulsion system is proposed.using our method,the efficiency and power of the system enhances without increasing volume and weight. This layout improves the performance compared to the usual layout, which employs double-armature motors in cruise speed where efficiency is more critical. This layout needs a complicated control system due to the difference of the motors. In this paper, first we suggest a type of complex controller and prove its controllability and stability. Then the control system is reduced to a simple system using the idea of low and fast dynamics separation. The non-linear MIMO system is split into two SISO systems, which simplifies the system so that the classical controllers would be applicable. Simulation results for both the classic and fuzzy controllers are also presented. A small model system which is built based on this approach, justifies the results.