heres what i do for movies on my ipad using handbrake...
even though handbrake has a preset for the ipad, i use the 'iPhone & iPod Touch' setting. i compared the two settings last year, and don't recall a glaring drop in quality for the 'iPhone & iPod Touch', though the file size was something like one half the size compared to the ipad setting, allowing for twice as many movies on my 64gb ipad.
when i use handbrake, i do the original import using the 'high profile' setting and rename the movie file with an '- hq' at the end (for 'high quality'), and then i do a second import using the first import as the source, but using the 'iPhone & iPod Touch' setting and renaming the movie file with an '- lq' at the end (for low quality). ((the moviename that handbrake discerns is sometimes cryptic, so nows the time to nemame it legibly)) this way i have a high quality version for home use where i have unending hard drive space, but for my ipad (where i dont have as much storage space) i have an entirely acceptable low-quality small-filesize version.
for the average movie the size of the low quality version is usually around 500mb, and the high quality version is about 1.3gb
for me on my system, handbrake brings in an average movie from the dvd in about 12-15 minutes at around 150-200 frames per second, and the second import comes in about 4 minutes around 500-600 frames per second. the second import goes a whole lot quicker since it comes from the hard-drive instead of the dvd drive.
when you doubleclick the finished moviefile that handbrake brings in, it will openup in itunes, and copy itself to the itunes media folder if you have the preferences set to do so. (this can consume drive space quickly. i set handbrake to place the movie on drive2, my itunes media folder is on drive3) the movie name in itunes will retain the '- hq' or '- lq' so you know which is which.
i then go to one of the 'cd cover' websites, and i pick out a neat dvd cover image for the movie, drop it into a 680x980 photoshop image file, bump the image around a little, and save it to a folder i made called 'dvd artwork' which i put in the 'pictures' folder, which is one of the apple pre-made folders (the one with the camera). (i name the all the artwork files dvd-moviename.jpg)
i then go back to itunes, highlight the movie, and click apple-i, and select the artwork tab, then click add, which pops up the pictures folder, where conveniently located is my dvd artwork folder (click the 'sort by date modified tab' at the top so you dont have to hunt for the image you just made), and i click the artwork image i made. i do this for both the hq and lq version of the movie.
i then sync the lq movie to my ipad, and voila, when i click the videos button on my ipad, up pops all the dvd artworks with the little reflection underneath too. really neat!