Did you set up the raid array in the bios itself first? I have only done raid on Intel boards and on those you must go into the bios and set the sata 0 and 1 as raid and then select raid 0. Then when you reboot the bios treats it like 1 HD. You should then get the default no operating system error. then your ready to install windows.
You might want to just disable the IDE or Pata channels in the bios altogether. It will free up an IRQ and might make trouble shooting a little easier.
On a side note the WD drives have a very aggressive timeout protocol. This makes raid on them a little difficult. If the drive does not respond right away the board will often mark the drive as failed and drop it from the array. WD charges an extra couple of bucks for thier raid edition HDs. This is a rip off because they are the same drives with only a more relaxed timming.