You can have them in your own folder, I do. I just make sure when it goes into the library it doesn't move the file.
iPhoto is fine for organisation, you've most likely buggered up somewhere. To go back to stage one delete the iPhoto Library folder within pictures (default). Then go through your folder/location that you use for pictures and ensure no duplicates. Then load up iPhoto again and it will recreate its iPhoto Library folder, before adding pictures ensure you go into iPhoto > Preferences and ensure "move to library" (or similar) is NOT ticked. It will then add the photo's into your library without moving them.
When you add in more pictures don't use the iPhoto picture importer, just move them manually into your own folder (organised how you want it), THEN import.