In this paper we discuss and compare two methods to control the free gyroscope seeker scan loop system: centralized control structure and decentralized control structure. First a centralized controller based on the linear model of the seeker is provided. We next proceed to design a decentralized controller using a non-linear model of the seeker. Input-output pairing is a vital stage in decentralized control and since the seeker model that is used in this structure is nonlinear, nonlinear RGA is used for input-output pairing analysis. SISO controllers are designed and proposed to track the specific scan patterns like conical and rosette.