Frankly I have no idea what you are doing or what is going on
A couple of notes
1. It is strongly NOT recommended to uncheck the preference to copy photos to the iPhoto library. It does not save space at all and has no advantages and many, many disadvantages
2. It is not clear what you are doing but remember that you only organize using iPhoto. You never make changes using the finder
3. Folders in iPhoto do not hold photos. They only hold other folders or albums.
4. For duplicates duplicate annilhator is a good solution. But again this is all done in iPhoto. Nothing is done in the finder
Having the iPhoto library on an external drive is fine and no problem. The problem comes is you uncheck toe preference to copy imported items to the iPhoto library which you appeared to say in your first post
" I do not have my photos copied because it's like double the size being taken up "
That is not a good idea
As to organizing. Use albums and folders. Not events