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I don't know that this is possible with the javafx public APIs.
You could attach an http://docs.oracle.com/javafx/2.0/api/javafx/scene/media/AudioSpectrumListener.html to both streams and try to blend the resultant data.
Not sure if the resolution would be good enough for your requirements or not and you would have to handle the re-encoding to another wav file yourself.
You may have better luck making use of the classes in the javax.sound package http://docs.oracle.com/javase/1.5.0/docs/api/javax/sound/sampled/package-summary.html, perhaps http://docs.oracle.com/javase/1.5.0/docs/api/javax/sound/sampled/Mixer.html is what you seek.
This is an equalizer, not a mixer, but some of the work here such as use of the AudioSpectrumListeners may be applicable => http://fxexperience.com/2012/01/fun-javafx-2-0-audio-player/