Do you know about "Paste remembers layers"? You set that in the layers panel menu. Then you can select all in the source doc, copy, and paste in place in the destination, and positioning will be the same. If there's already a layer with the correct name in the destination, ID will use it, otherwise it will automatically create the new one.
You have to do this page by page, but it might be scriptable.
Peter
I know that Ctrl Publishing had a plug-in for this, called CtrlLayers. It featured just that, export and import layers. It愀 not on their website any more, perhaps it愀 coming back.