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AMCL localizes the robot over the static map. It does not use the costmaps or costmap layers to do so, those are part of the navigation nodes. It is not clear why do you want to do a localization at the same time that you changes your map. AMCL does quite a good job in localizing the robot even if the current environment does not perfectly match the static map.

If you really need it, I would use a SLAM algorithm to localize your robot in a map that changes, but even then, such algorithm would eliminate dynamic objects from the generated map.

You should have no problem working with Jade and Kinect regarding layered costmaps.