Stay out of iPhoto in the finder. You will create havoc. iPhoto likes to organize the finder in its own way, and if you mess with it, you will certainly corrupt photos, lose photos, etc. Just do what ero87 said, and you will be fine. Just stay out of the finder!
It is really easy to organize your photos in iPhoto. The suggestions for folders and then albums is excellent. I also rename my film rolls to reflect what is on that roll -- sort of a first-line organization. You can also move photos from one roll to another for greater organization. For instance, I move most photos of my cats to one roll, regardless of when they were taken (the info pane will tell me that). Then I know that a single roll contains all the cat photos. Same for trips I take. While traveling, I often download photos to my MacBook during the trip, then erase the card in my camera so I have more room. Then download again after more photos. Then I combine those rolls so that they are all in one place, and the roll is named for the location of the trip.
Just stay out of the finder -- you will be very unhappy if you don't!