Hi Sean.
Just to clarify, VOD transcoding is not supported at present. What Andrew is describing is a work around.
The Scheduler Andrew linked to allows you to use a previously recorded file as a source for a Live stream. So essentially you are dealing with a live stream, thus you can run the stream through the Transcoder. Once you get the scheduler working, you will just need to follow the Transcoder guide for live streams.
How to set up and run Wowza Transcoder for live streaming
If the files are not located in the [wowza-install-dir]/content folder, you will need to modify the Application to point to the files. This is documented in the Wowza User Guide starting around page 54.
I hope this is helpful.
Regards,
Salvadore