No, you don't need to copy first to the internal drive. While I don't know anything about SuperDuper, and I don't know much about Macs in general, it seems clear that it is a disk cloner program that does not want to clone from a disk that is not formatted in HFS+ (Mac OS extended), either because it is not designed to be able to do that, or perhaps because the target disk may be HFS+.
BTW, the reference to "MS DOS" format undoubtedly means in more specific terms FAT32, which Mac OS's can work with, regardless of whether or not SuperDuper is able to.
My suggestion is that instead of bothering with the cloning utility, you simply use the file management provisions that are provided in the Mac OS to copy all of the files from one drive to the other. After doing that, as Toby suggested you should reformat the original drive, probably to HFS+, and then copy the files back to it. That would result in greatly reduced susceptibility to file system corruption, compared to FAT32, with the only downside being that it would no longer be compatible with Windows machines. If Windows compatibility is a consideration, you should reformat the drive anyway, after copying the files from it, but reformat to FAT32.
Regards,
-- Al
BTW, the reference to "MS DOS" format undoubtedly means in more specific terms FAT32, which Mac OS's can work with, regardless of whether or not SuperDuper is able to.
My suggestion is that instead of bothering with the cloning utility, you simply use the file management provisions that are provided in the Mac OS to copy all of the files from one drive to the other. After doing that, as Toby suggested you should reformat the original drive, probably to HFS+, and then copy the files back to it. That would result in greatly reduced susceptibility to file system corruption, compared to FAT32, with the only downside being that it would no longer be compatible with Windows machines. If Windows compatibility is a consideration, you should reformat the drive anyway, after copying the files from it, but reformat to FAT32.
Regards,
-- Al