That is not a simple program to use, but what you are trying to do is not just a convert file procedure, and may take some work to get right. A commertial tool may do the work easier, but I have not used them a lot so can't recommend one. Take a look here http://video-editing-software-review.toptenreviews.com/
There are tutorials available for AutoGK, http://www.doom9.org/index.html?/autogk.htm
is one good site. If you check out the root of that site, www.doom9.org you will find out pretty much all you ever need to know about working with video files. May take you a bit to wade through all the info though.