That's what I do, on my hard drive I create a folders named 1, VIDEO_TS, and AUDIO_TS. I rip the movie to the folder named 1. In DVD2One I select the folder 1 as the source. As for as output I select the VIDEO_TS folder and tick the CopyToDVD box and both DVD2One and CopyToDVD only burn the VIDEO_TS folder.
Are you saying I need to setup my hard drive like this?
E:\1 (used to hold ripped movie files)
and then in DVD2One's output box select E:\DVD_TS\VIDEO_TS