The way that iPhoto works is that unlike other photo managers (i.e., Adobe Bridge) is that iPhoto creates it's own unique library that is usually stored in your Pictures folder as a single file, where as other applications directly access the photos themselves in your User directory. When you import photos into iPhoto, it generally copies those photos into the library, or in your case since you have that option disabled, it creates a symbolic link, or shortcut much like the ones you would find on a desktop, to that file/picture that you imported. When you delete or move the photo from the location that it was imported, the next time you open iPhoto and try to access that particular file, it will open the shortcut, but the link will have nowhere to go and iPhoto will prompt you and ask if you want to find that photo. Essentially, iPhoto cannot sync with your filesystem as it maintains its own.
In my experience iPhoto isn't really the best for photography because of the way that it manages photos. It's really best suited for the casual vacation photographer who does minimal to no editing. If you're going to be using external applications, I recommend that you use an application, like Adobe Bridge, that works directly with your filesystem directory. If you want to continue using iPhoto, then I would recommend that you copy your photos into the iPhoto Library and set iPhoto to use external photo editors instead of the built in one. But that's just my honest opinion. Keep in mind tho, if you do copy your photos to iPhoto, then you will want to keep a backup of those photos separate from iPhoto. I've had instances where the Library file would become corrupt and I lost photos even after repairing the file.
Hope this helps. Good luck.