Another good tool for DVD ripping is DVD Fab.
I would suggest using a tool to Rip several DVD's (should only take about 15 min each),the ripped DVD will result in a Video TS folder. Then use the que in Handbrake and dump about 10 of them into Handbrake and let it encode over night.
You can use the ATV2 preset and the resulting file will play on both the ipad and the ATV2.
I have done over 600 DVD's like this and it works very well.
The only thing i would add is, if the DVD has subtitles on foreign language parts (movies like Star-Wars and The DaVinci Code have these) that you use the Subtitles tab and chose the "foreign audio search" drop down. I failed to do this and ended up having to re-encode several DVD's