After you bring a PCB into ACAD, type the explode command; I believe you need to do it three times before it says there is nothing left to explode. Save that to a new file.
Repeat this for the other PCB.
The two exploded files should load without disturbing each other.
You might also want to try a 'flat' DXF export from PADS.
If you don't need the AutoCAD functionality it may be easier just to import the two DXF files into PADS Layout instead of AutoCAD.
i'm not sure this will work but, 1st check to see if both boards are in mm or inches and have the same origin point. Export from pads in .dxf format one of the boards. Bring it into the AutoCad enviorment and then save it in .dxf format from AutoCad. Make a throw away copy of the 2nd board and import the .dxf into it. Make sure that you are working in the same mm or inches enviorment.