Layers are supposed to move by Holding the OPTION (alt) Key down when dragging them in Acrobat's Layer panel.
I'm not having any success with this if the Document wasn't created with layers and they are created by Pitstop (following JonasY's instructions).
I've read somewhere that Acrobat Layers are "Optional Content Groups" so I'm taking it that they don't work like layers in Photoshop, Illustrator, InDesign and Quark, in that they have no bearing on stacking order, objects just belong to a layer which can be switched on or off.
Hopefully someone from Adobe or Enfocus will correct me if I'm wrong