That's the part that isn't very easy to learn, as far as I know. You can use MPlayer/MEncoder and/or the mjpegtools. The transcode utilities may also be useful. If you're afraid of the command line, you won't like any of these options.
MPlayer CVS comes with some scripts for vcd & svcd converting in the TOOLS directory, but again, they're all command-line stuff and personally I don't even use these scripts anyway...