I hate to break it to you, but that board does NOT have a built-in hardware raid controller.
What it has is what is popularly known as FAKERAID, which is the same as any other mainboard under $700. The way it works is this; the bios will establish raid METADATA on the disks. This metadata will be recognized by the DRIVER. The raid function is ALL IN THE DRIVER! That makes it software raid.
Now in general, both software raid and TRUE hardware raid have their own advantages and disadvantages. Hardware raid has a performance advantage, software raid has a portability advantage -- means that if your mainboard dies, the disks can be inserted into any other computer and the data will all be accessible.
FAKERAID has NONE of the advantages of EITHER, and ALL of the disadvantages of BOTH.
Use the software raid option. Linux software raid is very stable.
Oh, and don't be expecting any major performance hit using software raid. The reason why fakeraid manages to pull the wool over on most people is because raid0 (and raid1 for that matter) really don't have any measurable performance penalty because they are so simple. In fact, raid0 will give you a wonderful performance advantage. Its only when you get into fancy stuff, like raid5 (striping with parity) that the performance hit becomes significant.