Assuming you are using Win XP:
1. Copy datool.exe to your Nexus directory.
2. Go: Start -> Run -> type: cmd -> Enter.
3. In Command Console type: cd [patch to your Nexus dir] - for example cd C:\Program Files\Nexus - The Jupiter Incident, then hit Enter.
4. Check if you are in right directory.
5. Type datool x nexus_00.dat -> hit enter.
6. After extraction move nexus_00.dat to backup dir (or it will overrule your changes) and play with files
This should work... Well... It works for me
Did you MOVE nexus_00.dat away from Nexus main dir? If this file and extracted folders are present, the game will load from nexus_00.dat.
As for file placement... just leave entire folder structure in the way it was created when you used datool, dont move files anywhere.