Hi markvr,
thank you for sharing your info...some of which I had already came across during my research 
I just started to play with the arduino and FFT and I am still trying to get it how it all works and how to set it up for my project..so every info will be welcome.
Btw, I have tried connecting things as stated before and it worked ok, but still had a lot of noise with this.
So I tried modifying this by adapting a circuit I've seen at Arduinoos' Didier blog http://www.arduinoos.com/wordpress/wp-content/uploads/MicroLS_05.jpg and it works like a charm..most of the noise disappeared (at least I no longer get a signal when no audio is coming out of the speakers).
