Reformat the hard drive as Mac OS Extended. You can't back an iPhoto Library up successfully on a drive that's formatted for Windows. And you can't copy two pictures that have the same name into the same folder, so forget about trying to export all your pictures to the external drive, unless you're going to rename enough of them to eliminate name duplications.
The only way to back up an iPhoto 6 Library and preserve all the albums, titles, books, keywords, calendars, etc. you've created in it is to copy the entire iPhoto Library folder as a unit. That eliminates any concern about duplicated names. But it requires that the drive you're copying onto be Mac-formatted, which makes the drive inaccessible to a Windows PC unless
MacDrive 7 is installed on it. Even in that case, there's no application you can run in Windows that understands the structure of an iPhoto database, so fnding anything in the library on the PC will be a nightmare. And worst of all, if a PC user moves or changes anything inside the iPhoto Library folder, it will be corrupted and become unusable in iPhoto. So if sharing pictures with Windows PC users is the object,
Export the pictures from iPhoto to the FAT-formatted external drive, and don't think for a moment that by doing so you've actually backed up your iPhoto Library — you've only backed up the individual pictures, not any of the organization you did in iPhoto.