IF you have a minute, www.hdcd.com good information there on this topic.
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I would suggest going from the transport to the digital in on the Sony. Personally I don't think the E9000ES is very good when it comes to 2 channel reproduction and hence even if the analog outs were better the A/D + preamp section would convert most any signal to two channel mediocrity. Of course if your transport has more than one digital out...you can hook up an analog and digital connection and A/B it for yourself using two of the E9000ES's inputs.