Depends on how you want your disc's file structure to look like.
(removed my crappy explanations)
edit: the CDRWin Help file
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Preserve Full Pathnames - Select this option to preserve the full pathname of every entry in the backup list. If this option is not selected, then the pathnames will be truncated to the root directory of each entry.
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Recurse Subdirectories - Select this option to recursively process all directories and files below the specified directories in the list.
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