Don,
I'm not an expert, but everything I've read leads me to believe that you are not listening to the SACD layer if you are bypassing the Sony's internal SACD processor.
Other than a couple of "hyper-expensive" transport/DAC setups that I've read about, no transports transfer SACD information via a digital connection. All SACD information is processed within the player and is only available via the analog outputs of the SACD player.
So, if you are letting the Proceed process the digital to analog conversion, you are likely listen to the CD layer of a hybrid SACD/CD.
Of course, if you are just listening to a redbook CD, I would guess that the Proceed just has a superior DAC to the Sony.
BTW, I have owned a Sony DVP-S9000ES and it's reputation as "an excellent CD player" is not well deserved. It may be a decent transport, but as a CD player it was easily bested by every dedicated CD player I've owned.
Enjoy,
TIC