PHP Code:

<?php
// This is code to run FFMPEG
// TECHNOLOGYFOREVER.COM
exec('ffmpeg');
?>

this what I have got so far I need to know how to get this to take a frame of the video, encode the video, and delete the other version which is not flv

I've never used this before, but you're using the exec() function which would be just like running the command in a shell. Here is the documentation to do pretty much what ever you should need to. http://ffmpeg.mplayerhq.hu/ffmpeg-doc.html