iPhoto contains its own "vault" for photos which, unless you've turned this function off in iPhoto, copies everything imported into it.
So if you have a bunch of photos in iPhoto AND folders in finder, you can trash the folders. They are now duplicates.
iPhoto's "vault" (library) is actually very easy to work with but relies heavily on ONE "golden rule" -- DO NOT mess with the internal assets of the iPhoto Library!!
When using iPhoto, the important thing to remember is that everything you may want to do to your photos can easily be done -- but only from WITHIN iPhoto. Need a copy of a picture? Open iPhoto, drag selected photo to desktop. Boom, you're done!
Need to work on a photo in, say, Photoshop? Set the preference for "external editors" in iPhoto, double click on a selected picture, BOOM Photoshop opens the photo. You edit, save and close Photoshop -- BOOM the updated picture is back in iPhoto.
You get the idea.