Motherboard SDIF Output Or Soundcard

Sound cards might reduce electrical noise, that can convert to time jitter of digital signal (especially with slow Toslink transitions).  This jitter appears as added noise (loss of clarity).  On the other hand Stereophile measurements of V90 show very good jitter rejection.  V90 also has asynchronous USB, that might provide better results (2-wire, no power USB cable).  Both, Toslink and USB are limited to 96kHz.  Again Stereophile measurements showed similar very low jitter with both methods.  If you're really happy with the sound, the leave it alone and enjoy.  One possible area of improvement is clean power supply.  My Airport Express, DAC and Power Amp are all plugged into Furman Elite-20 PFI conditioner with very good noise filtering.

At the moment I too use my computer as a source. I felt it best to avoid the sound card altogether and output via USB.  

+1 gdhal.
I, too use either USB or Spdif and output to a Schiit DAC.
One upgrade it did recently was to get Fidelizer Pro. It really made the sound reproduction much better.
Bob

As with gdhal and gdnrbob, I also use USB. I would consider the purchase of a used M2Tech USB to SPDIF converter which plugs directly into the USB port and run coax to the V90. No USB cable needed. This opens the possibility of purchasing a older used DAC having a more robust power supply and analog output stage as a further upgrade.