You have to work out your model in Blender and prepare it for importing through 3DX for animation.
Those extender bones for suit and belt were added for posing only and are not suitable for animation.
You could add those bones as extended in 3DX, but then you'd have to animate them manually for each character movement and clip (not efficient at all).
I suggest to get rid of them in Blender and apply weights to the belt which should be in sync with underlying suit mesh (and body mesh for that matter).
Regarding cloth going through another cloth, you could handle it with opacity maps, hiding part of the underlying mesh.
But I again suggest to handle it in Blender and delete faces before export (those you usually hide in CC). Or at least move outer cloth mesh a bit away from inner.