For VOD you can use something like Microsoft Expression Encoder 4 to encode the multi-bitrate renditions of the file.
For live streaming it is more bandwidth efficient to send one large stream to Wowza and have the Transcoder encode the stream and create the different renditions for ABR.
For the .smil file, you will need all the files of the multi-bitrate set located in the same folder as the .smil file, and you match the names of the files to the "video src" in the .smil file.
<video src="myStream_360p" system-bitrate="850000"/>
<video src="myStream_160p" system-bitrate="200000"/>