This paper presents a dual-stage control system design method for the rotational maneuver and vibration stabilization of a spacecraft with flexible appendages. In this design approach, attitude control system and vibration suppression were designed separately using lower order model. The design of attitude controller was based on sliding mode control (SMC) theory leading to a discontinuous control law. This controller accomplishes asymptotic attitude maneuvering in the closed-loop system and is insensitive to the interaction of elastic modes and uncertainty in the system. The shaped command input controller based on component synthesis vibration suppression (CSVS) method is designed for reduction of flexible mode vibration, which only requires information about natural frequency and damping of the closed system. Additionally, to extend the CSVS method to the system with on-off actuators, pulse-width pulse-frequency (PWPF) modulation is employed to control the thruster firing and integrated with the CSVS method. Simulation results have been proven the potential of this technique to control flexible spacecraft.