Basically most versions of HDMI cables are able to transfer both Audio and Video. on-board HDMI port is available only when you don't have any discrete graphic card on your motherboard. so when you use SLI/Crossfire the on-board HDMI along with the build-in GPU in your CPU will be automatically disabled (assuming you have a Core i series CPU).
When you connect your computer to your TV/monitor using HDMI cable you can also enable this feature to also let the sound transfer through it but you don't have to. there should be an option in your sound card settings to specify the output for the audio so in your case and for that particular motherboard, after installing sound card drivers, there will be a program named "Realtek HD audio manager" that has the option to change the audio output. it can be changed through Windows sound settings too.