Install one drive, unless your doing raid. Boot to the windows install disk and follow the prompts to load windows. Once windows has loaded you can install the other drive. I do it this way so you don't mix up the drives and install on the wrong one.
If you are doing raid then you need to enable the raid controller in the bios, then go into the raid setup after the post screen and set the drives to how you want them: Raid 0 or Raid 1.
Make sure you have the drivers for the raid controller on a floppy to load at boot if using xp, not sure about vista. You will then press F6 during the windows setup to load those drivers so the windows install will see them. From there you will load windows like normal.