AnyDVD to an MKV file question



I have my anydvd running in the background and can copy and paste my m2ts files to play on my wd tv with no problem. What I am having a hard time is that the m2ts file does not seem to carry the forced subtitles(the ones you see when an alien in a movie speaks or other forced subtitles). It also only seems to carry the AC3 audio. I was told that if I wanted the forced subs and other audio tracks I need to put them into an mkv container.

My question is which program do I need to do this with, and how do I know which files are needed to creat this mkv container?