I run my PC's optical output into a DacMagic+. Totally bypasses everything.
Never thought about disabling onboard hardware.
My onboard sounds pretty darn good, even through el cheapo patch cable, a different sound to the DAC, but I wouldn't like to say worse.
I've got a full-on gaming rig, with a Marantz PM6000 and Mission 751s bringing the big noise. I spend more time at the PC than anywhere else, so I gave it a sound setup to match
Perfectly happy with my onboard- although I bought the DAC, so I'm gonna use it! Does vary by motherboard though, shielding, interference susceptibility etc.