Theyre not too difficult to find. Good stuff on Doom9 and flowplayer forums. I realize that the appeal of zencoder is that you don't need to understand ffmpeg's elaborate settings, but its sorta fun to dig around and see what each one can do. Lots of technical algorithmic challenges in encoding.

For a good practical guide, I suggest reading this: http://www.amazon.com/H-264-MPEG-4-Video-Compression-Generat...

It'll give you an idea of where all the settings come from.