I write this one only because the first time I burned a disc with CloneCD I got freaked out that I may have checked the wrong thing and ruined a CD. Good thing I guessed right the first time!
Anyway, if you go the smart route and burn a small 10-20MB image to work with, then change the Image.ccd file to whatever you want to burn, you'll probably get the same message pop up just before the burning starts that I did (ver3). It asks if you want to:
+ Keep ToC as on source CD, write until end of Image File. O Modify Lead Out address to the length of the Image File.
Choose to Keep ToC as on source CD ... it works out correctly that way. Otherwise it will mess with the CCD file and you won't get what you're expecting! Just wanted to pitch that in for anyone who doesn't have experience with it yet so they won't freak out like I did.