The Maya FBX Plug-in now gives you the choice to import layers from MotionBuilder without baking the animation layers. Doing this preserves MotionBuilder-created key framed animation layers on import into Maya. Otherwise, the animation is baked into a single animation layer.
To retain MotionBuilder animation layers as separate layers in Maya:
If the option is active, the plug-in automatically bakes the animation layers during the import process.
This workflow is only for importing MotionBuilder-created FBX files to Maya 2009. Layers created in Maya do not export to FBX but are instead baked automatically.