Although I'm a big fan of iVI, I haven't managed to get it join files properly, there has always been an audio issue.
In your case what I would do is use a programme called
MakeMKV, although it looks very Windows based it does a great job of taking either a DVD Disc/ISO/VIDEO_TS and creating an MKV file. When creating the file you untick all the audio & sub tracks not required so if you have a movie over 2 DVD's you can get them set exactly alike.
Then I would use
MKVtools which does a great job of joining them both to create one big MKV.
Finally drop that into iVI for a fully Metadata'd M4V to view of on the AppleTV.
It's a bit of a long process but there shouldn't be many multi disc DVD's so shouldn't take too long.
