A computer-assisted medical system comprising: a plurality of manipulators (102a, 102b); a user input system; a user output system comprising a display device (107, 107b, 107c); and a controller configured to execute instructions to perform operations, the operations comprising: in a pairing mode and in response to a first set of signals generated by the user input system, causing a virtual selector shown on the display device (107, 107b, 107c) to move relative to imagery shown on the display device (107, 107b, 107c), wherein the imagery represents a location of a first instrument supported by a first manipulator of the plurality of manipulators (102a, 102b) and a location of a second instrument supported by a second manipulator of the plurality of manipulators (102a, 102b), in the pairing mode, providing feedback indicative of a recommended association between a portion (108a, 108b) of the user input system and the first manipulator, in the pairing mode, associating the first manipulator with the portion (108a, 108b) of the user input system based on movement of the virtual selector relative to the represented location of the first instrument, and, in a following mode, controlling motion of the first instrument in accordance to a second set of signals generated by the user input system in response to operation of the portion (108a, 108b) of the user input system by a user. a plurality of manipulators (102a, 102b); a user input system; a user output system comprising a display device (107, 107b, 107c); and a controller configured to execute instructions to perform operations, the operations comprising: in a pairing mode and in response to a first set of signals generated by the user input system, causing a virtual selector shown on the display device (107, 107b, 107c) to move relative to imagery shown on the display device (107, 107b, 107c), wherein the imagery represents a location of a first instrument supported by a first manipulator of the plurality of manipulators (102a, 102b) and a location of a second instrument supported by a second manipulator of the plurality of manipulators (102a, 102b), in the pairing mode, providing feedback indicative of a recommended association between a portion (108a, 108b) of the user input system and the first manipulator, in the pairing mode, associating the first manipulator with the portion (108a, 108b) of the user input system based on movement of the virtual selector relative to the represented location of the first instrument, and, in a following mode, controlling motion of the first instrument in accordance to a second set of signals generated by the user input system in response to operation of the portion (108a, 108b) of the user input system by a user. in a pairing mode and in response to a first set of signals generated by the user input system, causing a virtual selector shown on the display device (107, 107b, 107c) to move relative to imagery shown on the display device (107, 107b, 107c), wherein the imagery represents a location of a first instrument supported by a first manipulator of the plurality of manipulators (102a, 102b) and a location of a second instrument supported by a second manipulator of the plurality of manipulators (102a, 102b), in the pairing mode, providing feedback indicative of a recommended association between a portion (108a, 108b) of the user input system and the first manipulator, in the pairing mode, associating the first manipulator with the portion (108a, 108b) of the user input system based on movement of the virtual selector relative to the represented location of the first instrument, and, in a following mode, controlling motion of the first instrument in accordance to a second set of signals generated by the user input system in response to operation of the portion (108a, 108b) of the user input system by a user.