Your use of "keep" is not fully appropiate, I'm afraid, if your current organisation is more chaotic than you want.
So my advice:
1. Start designing the right structure for your needs (folders and subfolders).
2. Then make it, all empty.
3. Then just start moving all those files to their right place. If Windows Explorer says there's a duplicate, rename it and see for yourself which of the 2 you want to keep (or maybe both with a different name).
Takes some time, but it's the best way.
I'm good with computers/tech, but i have photos/docs scattered, duplicated all over my computer. Id like a program to help me sort them, remove duplicates. I know I should have placed them all in perfectly organized folders from the beginning, but I didn't. Let me know.