How do I remove a single chaptor from being burnt to a DVD within CloneDVD2 (like the entire movie minus the ending credit chaptor)?

Also, when I get to what audio I want to have included on the DVD, how can I tell which audio track is the commentary or the normal movie audio?

dont quote me on this but i believe that either of those options are available right now with elby's clonedvd2

You can do both...

I sometimes cut off the ending credit if it possible, When you are in the preview screen just click on the little scissors and you will see the individual chapters, just slide the bar.

as for the commentary, someone else will have to answer that because im not totally sure how but it can be done

i never knew that about the cutting out part .. haha

I have only used it a couple times, with a movie that was really large and the compression was just too much for me, I call myself cutting out every little piece that was not needed to bring it up. Some movies carry over into the credit's and if you cut that, you are cutting out the end of the movie, not too many movies let you just cut the credits as a chapter. Maybe some new Version of CloneDVD will let you choose the point of cut off instead of chapter cutoff.

Chapter Removal

AC3/2 is usually the commentary ( read the manual or search the forum ! )
Preview it using CDVD2 has so far been impossible and the matter been discussed many times.
You can always use DVDShrink for "previewing" the audio streams.