Edited by Qoweg - 6/30/14 at 8:16am
First off, when you use an external USB DAC, it's bypassing your onboard sound, so you don't have to worry about your onboard sound card anymore.
The Nuforce uDac and iBasso D2+ are both USB DACs and they will also drive your headphones.
The difference between the USB and PCI version is that USB is external, PCI goes in a PCI slot inside your computer. If you're asking for the difference between the models, that information should be on the product website.