Yes, do follow the JW Player dynamic streaming tutorial. It’s a client-side solution. The only server-side aspect is the BWCheck module and the stream variations.
You can use remap a stream in an application module or use StreamNameAlias possibly to help with your use case:
Override play remap stream name
https://www.wowza.com/forums/showthread.php?t=6876
StreamNameAlias
http://community.wowza.com/t/-/47
We’ve been testing Expression encoder recently and it seems to be producing correctly aligned versions.
Richard