Yes, these graphics cards have a SPDIF input connector on them, so you would loop from the SPDIF output connector (on the motherboard or sound card) into the SPDIF input connector on the graphics card (they generally use coax). The output should be full HDMI including DD 5.1 and stereo over the cable.
There is a motherboard on the market that uses an integrated graphics chipset with HDMI integrated, along with an integrated HD-Audio controller. As a result, you don't have to jack audio into it as it grabs audio directly off the PCI Express bus. I would imagine this to be the trend for graphics cards as well, meaning that this SPDIF input connector will not be needed as the graphics chip will be able to pull audio directly out of the PCI Express bus. Doesn't get much cleaner than that!