For starters, you will probably have to point php to your ffmpeg install. Not sure where that would be on a windows system, but in linux, you would use something like
$ffmpeg = "/usr/local/bin/ffmpeg";
Then to actually execute your conversion, use something like
$exec_string = ($ffmpeg . " -i " . $uploadFilename. " -b:v 2000k -acodec libvorbis -ac 2 -ab 256k -threads 0 " . $finout . "");
Obviously, you need to set the variables for the original file name ($uploadFilename) and the name of your newly created output file ($finout). But that works for me. And depending on how you installed ffmpeg, you may find that you need to reinstall it. There are a variety of addons/extra codecs. For myself, I found the basic ffmpeg install would have issues with webm. I needed to install it with additional codecs activated.
There's a good tutorial for that here
Be sure to follow all the "optional" steps as well.