Disclosed herein are systems and methods for controlling robotic apparatus having several movable elements or segments coupled by joints. At least one of the movable elements can include one or more mobile bases, while the others can form one or more manipulators. One of the movable elements can be treated as an end effector for which a certain motion is desired. The end effector may include a tool, for example, or represent a robotic hand (or a point thereon), or one or more of the one or more mobile bases. In accordance with the systems and methods disclosed herein, movement of the manipulator and the mobile base can be controlled and coordinated to effect a desired motion for the end effector. In many cases, the motion can include simultaneously moving the manipulator and the mobile base.