The 8 Channel HiDef audio on your board is indeed very good for HiDef audio. However as you have mentioned it all depends on the speaker setup that you are using. If you are feeding the audio to a receiver via an optical cable then go for it. The on board card will do wonders. If you are just feeding it directly to a monitor that has build in speakers then you should just keep the HDMI for it is simple and fully digital. However there is one draw back still. The HDMI audio doesn't have the same EQ controls that you would get from feeding it from your motherboard. But I personally think there is no replacement for fully digital audio e.g. optical or hdmi.
Just assembled my first custom build and a perplexing question came to mind. Which way would I get better sound?
I have an Asus Sabertooth 990FX R2.0 with Realtek 8 Channel HiDef audio and I have a Nvidia GTX 560 Ti card. At the moment I'm running sound through the hdmi from the graphics card. Would I be better off keeping it that way or running the sound through the motherboard outputs? I know it may depend on my setup: speakers, etc. But all in all which one should put out better sound?