I have the same thoughts. Sound is everything. I use both opticals on the Audigy NX SPDIF from NX to Eclipse Deck, the other Optical is for Sirius Radio and run 8v from my eclipse deck to the MTX amps so 0 noise and clear sound.
I chose the NX because I wanted the single PCI slot on the Epia board for a graphics card.
Sound is awsome, however the NX takes extra CPU power, and after almost a year of it running in the car I never touch the NX. So if you dont need that PCI slot I would go with a PCI sound card. Dont forget if you need a MIC and the computer is in the trunk this is another hurdle to over come.
Both ways you cant go wrong really, try and use optical as much as possible.