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Disable CMSS in the EAX console.
In Speaker Settings select 5.1 Speakers, leave Digital Output Only unticked (Otherwise you'll only get 2 channel output).
Bass Redirection can be left Unticked (The Logitech system can control that itself).
The Creative Equalizer should be disabled.
As regards Surround Mixer, leave the Bass/Treble controls at their default levels (50) & set the Master Volume to something less than 100% (0.0dB) - recommended by some to go as "low" as 75% (-7.5dB) with it. The other sliders set to whatever you want.
In Audio HQ -> Device Controls -> Decoder tab select SPDIF Passthrough & set your DVD decoders to SPDIF Output also.
For media player try switching to Foobar 2000, I've a guide on that which should be posted soon.