The trick (and the beauty) of iPhoto is that once the photos are stored in iPhoto, ANYTHING you might want to do to them, and I mean *anything*, is done from within the program.
Let the computer do the file management. That's what you bought a computer to do. Your job is to a) learn the program and b) make sure you have good backups. Beyond that, you don't need to worry about how iPhoto handles things, because ANYTHING you might want to do to or with your photos is handled *within iPhoto.*