Reading the manual which is installed with CloneDVD by clicking "help" might... help.
Here is a quote:
Splitting: If you want to copy the whole DVD or you want to copy a movie with extra length, it is advisable to split it over two DVD media. First of all you have to select â€œpreserve menusâ€ for keeping the overview. Via the â€œchapter cuttingâ€ function you can split the main movie in two parts while selecting for example the chapters 1-9 for the first DVD media. Select now further titles like â€œSpecial Featuresâ€ and start the copying process for the first DVD media. When the copying process has finished, please click on the â€œBackâ€ button until you reach the window with the title selection. Please click with the right mouse button into the title selection dialogue: You can invert your selection for the first DVD media, like in this example, it means that the chapters 10-16 of the main movie and the rest of the titles will be automatically selected
HINT: If you want to split a multi-angle movie, please cut off the same chapters for each camera angle. You can easily recognize titles with different camera angles, as they all have the same playing time!