Its okay, i understand what your getting at, adding the files manually to the video_ts folder will not work, however as i have said its easier to let nve3 recode these files or more accurately let nve3 create a menu for your multiple files. Using add video files select the video_ts.ifo file from the video_ts folder and nve3 will then have added the video file, now go back to add video and select the other video_ts.ifo file from the other video_ts folder, and so on until nve3 lists all your video files. It dont matter when importing if all the files have the same name because the original locations will all be different. Then hit next button and create a menu to access these videos. Choose hard-drive folder and not burn direct to disk, this way you can check to see if this has worked correctly.
To add files manually, the only way to do this is to use ifoedit and edit the ifo file and point to the various vob files:
Add additional files as
and so on
However info on how to do this, i cant help with, since i've never used this program, its just easier to use nve3 to put these vob files all togeather.