Example:
-Two frames on a layout, one on left and one on right
-10 data driven pages
-It would display DDP's 1, 3, 5, 7, 9 in the left frame and DDP's 2, 4, 6, 8, 10 in the right frame, for a total of 5 sheets of paper.
I just experimented in ArcMap 10 with two data frames with DDP's turned on and it only updates one of them, the other remains static.
If both of your data frames have the same extent (but display different layers) you could do this. See the following help topic:
http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#/Customizing_your_map_extent/00s900000011000000/
Your scenario can be accomplished with the arcpy.mapping scripting environment. You would set the two data frame extents independantly using whatever method you need.
Jeff