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I'll just add that you can give goals to the navigation stack in whatever frame you wish. If you always want to send goals relative to the robot's current position, using the "base_link" frame should be fine. Sending goals in a global frame like "odom" or "map" is normally the right thing to do when you have some specific position in the world you want the robot to move to.

Another thing is that the velocities reported by odometry are actually in the robot-centric, or "base_link" frame, so you don't actually have to rotate them to reason about them in that frame. The Odometry message is sort of funky in that way, but is documented here: http://www.ros.org/doc/api/nav_msgs/html/msg/Odometry.html.