this thread may help http://club.cdfreaks.com/showthread.php?t=91718&highlight=commentary
basically AC3/6 is usually the main movie
AC3/2 is usually director's commentary
DTS takes up a lot of space and is useless if you can't play it back on your speakers.
PCM takes up the most space and I'm not sure what it's for.
if you have dvd shrink you can preview the audio for reference (right click in the preview window to switch to and preview audio tracks) then make the correct selection in clonedvd2 (they will be listen in the same order). clonedvd can not have this feature because of licensing fees that must be paid for playback of Dolby material.
also the audio streams in any palyback software (powerdvd, vlc, etc) are usually listed in the same order when you right click to change audio as they are with clonedvd2.
if you're unsure if you've made the correct selection, output to files or image then palyback from your hard drive to double check before burning and wasting a disc. if it's correct then just use clonedvd2's "write existing files" option to burn. if it's wrong, just delete it.