There are many different ways to convert to or from MKV files. Personally, I use MediaCoder. It allows me complete and total control over my conversions. If you need help with MediaCoder, I have posted a ton of help for it all around the forum. You may have to search, or just ask me again; I'm glad to answer your questions.
http://mediacoder.sourceforge.net/
If you want a simpler program you can try out RealAnime. It was made specifically to transcode files into MKV containers.
http://www.softpedia.com/get/Multime...ealAnime.shtml
I haven't used it myself, but you may like it.
Enjoy! ;-)