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any way to reorient the control sphere so the atom can be manipulated in the exact direction you need? detach works until you reattach, then the atom just moves relative to the input from the old orientation.
You can parent your atom to another and then move the parent instead?
Otherwise try PowerHandles (plugin out of Essentials package). That supports switching to global orientation (rather than local), which may be similar to what you want when you got a rotated atom but want to move/rotate it relative to the global orientation of the scene.
Parenting basically means: "Glue this stuff together as this angle and distance". As long as you move the parent object, the child object moves with it.