You could take a look at the ILiveStreamTranscoderNotify and ILiveStreamTranscoderActionNotify interfaces. and dynamically choose your template file. Setup the following event handlers as indicated in this post. Then you can choose the template required by leveraging the liveStreamTranscoder object within the ILiveStreamTranscoderActionNotify.onInitBeforeLoadTemplate event handler as follows:
liveStreamTranscoder.setTemplateName("TemplateName.xml");
Regards,
Salvadore