The onboard sound card has ZERO effect on the quality of the audio. The bits are traveling directly, unmolested from the application generating them to the amplifiers in the speakers.
That's what I thought for a long time and then I discovered that I was wrong (so you are - no offence).
Digital sound can be altered on the way between application and the DAC interpretation, even with TosLink (optical).
Have a look about the clock jitter problem, or phase noise