You need to transcode the videos to the required bitrates manually by using a transcoder.
ie sample.mp4 to sample_240.mp4, sample_360.mp4, sample_720p
Wowza do not have VOD transcoder by this time. Since you are using AWS S3 buckets, I'm suggesting you to transcode all the videos using AWS Elastic Transcoder.
You should create two S3 buckets. let's say : uploadvideofiles, transcodedvideofiles
You need to upload all of your videos to "uploadvideofiles" bucket and by using transcoder you need to transcode it and save in the "transcodedvideofiles".
Here is the AWS Elastic Transcoder Guide : http://docs.aws.amazon.com/elastictranscoder/latest/developerguide/introduction.html
Now you can use the transcoded videos for streaming.