My mother tongue isn't English, so bear with me.
First of all, I would like to thank the people involved in making the critically commenting subtitles. Great job!
Next, in order to make Expelled play with these subtitles, I suppose you need Expelled as an avi-file AND re-name the subtitles file exactly in accordance with the movie's name (exepting the extension, in my case respectively .avi and .srt. - E.g. 'Expelled_critically commenting subtitles.avi' and 'Expelled_critically commenting subtitles.srt'). It works fine for me, using Media Player Classic.
Finally, since 2004, I have worked as a Philosophy and Theory of Knowledge (TOK) teacher in the International Baccalaureate (IB) system, and besides, I've taught Literature, Antiquity and Philosophy in my national educational system, in fact since 1976.
When some months ago I first watched Expelled, I thought "This seems interesting...". Now, having watched the movie a couple of times, and having visited a good deal of critical internet sites, I'm disappointed, embarrased and horrified on behalf of the Intelligent Design movement, and on behalf of honest Christians respecting Science as an independent realm besides the independent realm of Faith.
As far as I have been able to scrutinize things, Expelled is one of the most manipulating 'documentaries' I've ever watched.
For my teaching purposes, I've set up a web page on Intelligent Design vs. Evolution in general. However, it's a work in progress, and I have not had the time to update it with references to the subtitles materials at stake. Nevertheless it may be of some interest to members of this forum: http://kj.kolding-gym.dk/TOK%20archive/intelligent_design_andor_evolut.htm