What I'm saying is that this is entirely up to you. It has no impact on the mod. You can decide what you want the template to be for your mod pack on your own.
Personally, I'd use folders so it's easier to see how many I have for different chunks. Like:
Race/Sex/Age/HairFur-Eye-Tits-Ass-misc.png
and an example
Human/Female/Adult/Blond-RedEyes-TitsB-AssS-1.png
Again however, this is entirely up to you.
I'm tempted to write a portrait pack manager app. Lets you select a portrait, view it, and then edit the tags, and it renames both the portrait and body in-sync. Maybe even let you select an image as full body, select a section to crop as portrait, and add that? What OS do you guys use? My language of choice for such an app would probably be C#, the result working on Windows, and maybe on Linux/Mac via Mono. Probably make your work of renaming them a lot easier, as you'd just have to select an image, check some boxes, click apply, rinse repeat for folder.