There should be nearly no difference, technically HDMI can carry Digital signals and then your device is the DAC (a DAC turns digital sound into analogue sound which is the things you hear (basically))
Whereas your onboard sound card on your motherboard acts as the DAC and delivers it straight to your speakers.
So technically they should be about the same. Depending on the motherboard DAC and if it is also an AMP.
HDMI can support 7.1 speakers but seeing as you're just using stereo, again there should be nearly no difference. You are using the audio jacks on your motherboard right?
I would use the onboard motherboard sound as it usually has more effects.
-good luck