No, you would use FFmpeg as the transcoder. I do not think you would need the Wowza Transcoder in this workflow. This is not documented anywhere and I am not exactly sure of the workflow.
This guide is helpful, but does not address your particular needs:
Frequently requested FFMPEG command examples for Wowza
You may find someone you can hire to help get this setup in the find a consultant forum
Kind regards,
Salvadore