Years ago we used to be able to do this, since the Vismock up and the teamcenter viewer overlay is really good, we have stopped using the PDF overlay. If you google PDF overlay compare you will get some hits. Also you can use the track drawing changes that was introduced in NX8 or NX8.5 which works really nice which has an overlay also.
years ago we used a Adobe acrobat writer, to do our compares with. I can not find the functionality in the Adobe Acrobat we have today.