Space manipulators mounted on a free-floating base are structurally flexible mechanical systems. For some applications, it is necessary to control the attitude of the base by the use of on-off thrusters. However, thruster operation produces a rather broad frequency spectrum that can excite sensitive modes of the flexible system. This situation is likely to occur especially when the manipulator is moving a big payload. The excitation of these modes can introduce further disturbances to the attitude control system; therefore, undesirable fuel replenishing limit cycles may develop. To investigate these dynamic interactions, the dynamics model of an N-flexible-joint space manipulator is developed and used to describe a three-flexible-joint manipulator mounted on a six-degree-of-freedom spacecraft dubbed in this thesis "spatial system". Since the attitude controller assumes the use of on-off thrusters, which are nonlinear devices, the describing-function technique, an approximate method for the analysis of nonlinear systems, is used to analyze four different control systems using an approximate two-mass system. This technique is adapted to be used in conjunction with the root-locus concept, thus providing a different picture of the problem and helping in the control system design. A parametric study is performed to compare the control schemes using those analytical tools, which is validated with simulations using the spatial system. It is shown that the three proposed variations of a classical control scheme are very effective to minimize such undesirable dynamic interactions. Finally, Mecano, a commercial mechanical-system modelling and analysis software tool, is adapted for the study of control systems and used to study the effect of link elasticity on the robustness of the proposed control schemes.