Right, I also use the portrait editor. It works wonders. When you use the editor it will make the sructure Race-Female-Age. Which is a good folder structure and Ive never seen it fuck up. What ive personally done in the past is basically this:
Look through folders for duplicates
If no duplicate move it to seperate folders marked P or B
once done name all something like "1" or "A"
Delete the old race folder. Then edit the images, move them back to the Bodies/Portraits folder. This helps since theres no foolproof image duplicate software thats any good, unless you want to pay. However, it becomes increasingly tediious with larger sections like Human or Elf.
As for the issue of the full bodies, as long as they are in identical folder paths, there wont be an issue. However one mistake and it doesnt work. Heres an example of what basically happened to Arachna in my last reply.