Do you need to remove the Xonar in order to compare? Cannot you run onboard audio alongside the Xonar?
Might depend on the board I suppose. I have no problem running onboard audio and a sound card in my system. In fact, I don't think I've ever had a PC, where I could not use onboard audio and a sound card simultaneously.
Would make it much easier to compare, if you can just switch between them in the Windows sound options.
The difference between onboard audio and a sound card should be more discernible when using headphones. Onboard audio more often than not, does not provide enough amplification for a lot of headphones. Speakers are a different matter, as they have an amplifier.
Using my Goldring headphones with onboard audio, they sound crap and dull in comparison to when being used with a sound card.
Will not you use the Dolby Headphone feature of the Xonar? You won't get any surround sound from your headphones, if you switch to onboard audio.