Right - first off - if you are backing up a commercial DVD, you need to have AnyDVD running, this will remove the protection from the disc on the fly. You then need CloneDVD2 to make it fit onto a single sided disc.
With AnyDVD running, load the original into your drive. Start CloneDVD2. On the first screen of CloneDVD2, select the first option Copy DVD Titles.
This will take you to the second screen - on the click down arrow select browse - find the Video_TS folder on your DVD disc. It will now allow you to select what video titles you want (it will automatically select the main movie) - you can also preview the video here.
Click next, and select what audio stream you want - click next again - and now your on the output method screen. To burn to a disc click on DVD writer on the top right of the screen. (you may have to tell clone where to store temparory files)
Now click on go -
follow this and let me know how you get on.