I believe you start deleting photos.
The iOS file system in regards to photos dictates a new folder per "X" amount of pictures taken or stored on the phone. The locations of the photos are referenced in database files (Photos.sqlite series of files) in the PhotoData folder (which you'd need an app to browse) and so moving your photos collectively into one folder would almost certainly throw this off.
This may be disorganized to you, but it's Apple's filing system. I'd leave it alone. The alternative (after messing it up) would be having to delete the Photos.sqlite files which would cause your entire camera roll database to rebuild and would result in a new series of folders.
