Here is my process....... (might not be the most efficient)
I play the movie/show with an ordinary DVD player, and look to see if the disc automatically chose a subtitle setting, if it did I select that in handbrake.
The newest handbrake (released a few days ago) and I think the previous version has a selection under subtitle called Foreign Audio Search (Bitmap). I turn that on, it scans a movie/show, and if it one that forces subtitles only during certain scenes it will pick that up... (kill bill, defiance, boondocks saints 2 come to mind for examples.)
http://trac.handbrake.fr/wiki/Subtitles for more info.
I always hard burn them in to the video, I don't think iPads, apple tv's etc can use selectable ones.