They should be exactly the same. In both cases, neither the sound card nor the motherboard is doing any decoding (at least not in the digital to analog conversion sense). Either one will simply take digital audio samples and pass them to your receiver.
I think your concern about audio quality is about the question of digital to analog conversion. I will generally offer that a receiver or a preamp will do a better job of digital to analog conversion than a PC soundcard or on-board audio. I might describe the analog signal as more "fragile" than the digital -- it's more prone to noise and interference than the digital samples. Therefore, when the analog signal is handled in the very noisy environment of the computer, it might pick up noise. Also, most soundcards and such are relatively cheap, and use cheap components to handle the analog signal after the conversion. This again leads to noise in your audio. I have a PC connected to a receiver in my office on an analog output and if I turn the receiver up all the way with no audio playing from the PC, there will a very high noise floor (a lot of hiss coming from the speakers). If I do the same thing with a good analog source (e.g., even a cheap CD player), there's very little noise floor.
Your Sunfire will definitely do a better job decoding the signal. Hook either the soundcard or the motherboard optical out to it and go for it! Actually, hook them both up and switch back and forth. You should not be able to hear a difference. If you can, I'd think that there is something wrong in the soundcard settings or drivers. You can also compare it to the analog output and see if you can hear a difference.
Of course, there are high end sound cards that have been engineered to avoid the problems I discuss above. But, chances are that unless you've specifically searched out such a high end sound card, you have a cheapy model, and the above discussion applies.
Also -- all this "which sounds better" discussion is dependent on your ears and the resolution of the rest of your system.
Good luck!