Copying back-ups

Hi,
I've searched all over the net and I still can't seem to find any decent guide to the best way of copying back-ups.
Is it possible just to clone the CD with CloneCD? Will self-boot games still be self boot if you do this? What settings should be used?

I managed to make myself 2 self boot DC disks (A MP3 player and a Mega Drive emulator) - could I just copy the files off the CD then use this method to make a self-booting copy of a back up?

Thanks in advance for your help!