Automatic organization is leaving the problem to someone else. Again, you want control. You want to be sure that it's done your way because you are the one who will be using the photos and you want to be sure they're the right ones.

I would probably approach the problem as follows:

Connect a fresh clean disk and create a folder 'Archive' or some such name. Copy ALL the photos into that folder. Then go through the process of identifying duplicates and selecting the one you want to keep. Copy them to a new folder structure and try to organize them in that structure. That way if you screw up the duplicate cleaning you still have your old photos where they were originally. When you've got your photos organized to your satisfaction, delete the old copies of the photos and copy the new folder structure to your primary location. Then save the scratch disk as part of your backups.