I didn't know that a graphics card had an on board speaker. I'm a bit skeptical of this. Anyways, the beeps will come from a small system speaker in the case. Along with your power and reset connectors there should be a speaker one. It will connect to the bottom right side of your mobo. page 2-34 in your manual will explain this. As long as you have this hooked up, and you probably do, that will give you all the beeps that are occurring.
Actually, your board doesn't technically have on board sound. According to the manual I read, it has a sound card that sits in the PCIe x1 slot. This card, however, has nothing to do with the beeps you hear during P.O.S.T.
[EDIT] After reading your case manual, I fail to see the speaker pin I am talking about. Every case I have worked in usually has the 4 pin speaker connector. the manual doesn't have instructions including this. It only has instructions for hooking up the front panel audio. Hopefully someone else on this thread has that case and can enlighten us both. If not, my friend has that case and I will check with him tomorrow if no answers are posted before then.