After importing both files into Unity, you should see a animated character in the preview window when selecting the animation FBX. And yes, you should animated on the rig controllers, unless there's something really specific that needs animation on the bone directly.
Be sure to ‘bake’ the animation on the bones export, so Unity knows what to do with it.
But normally (in Maya) you would export the (static) bones + geo as a separate file, and just the bones for the second file.
RobW Cannot open the rar file, it is corrupt or created with something else than Winrar? We're looking into this as well atm, and could be a interesting discussion to have.