Systems and method are disclosed whereby elongate medical instruments may be registered to adjacent tissue structures and other structures, and may be navigated and operated in a coordinated fashion to maximize ranges of motion, ease of use, and other factors. A method for registering an instrument relative to nearby structures may comprise moving a portion of the instrument between two in situ positions, tracking movement during this movement with both a kinematic model and also a localization sensor based configuration, determining the orientation of the tracked portion relative to both the instrument coordinate system used in the kinematic modeling and also a localization coordinate reference frame, and adjusting the orientation of the instrument coordinate reference frame to minimize the difference between determined orientations using the kinematic model and localization sensors. Methods and configurations for navigating coupled and registered instrument sets are also disclosed.