You may be referring to the originals say in a folder on your desktop and then copies in iPhoto directory.
If this is the case, check your preferences in iPhoto and see if you have asked iPhoto to copy photos from original source to iPhoto. If it is NOT, delete your iPhoto copies (via iPhoto and empty trash in iPhoto. Do not use Finder) and reimport with this option selected. If you don't copy to iPhoto, iPhoto will refer back to the original location which is a pain in the A** (iPhoto creates alias' or some crap that makes links to originals). If it is checked to copy into iPhoto, move the folder of the original source somewhere else and check to make sure iPhoto still works. If it does you can delete or move off the orginal source (desktop folder as example) as you have two copies, one in iPhoto Library and one on desktop.