In the power management, try setting drives to spin down after 3 or 5 minutes. Windows will power up the specific drives on demand and spin them back down when not in use.
Thats not 100% true.. I use the same spin down feature for windows. For my PATA drives, when I access one, they both will spin up. And since one is a little older than the other, I usually find myself waiting for both drives to get to full speed so I can access my data (yeah 10~15 seconds wont kill me.. but when you are "in the mood" its a life time....) Sata drives do not suffer the same fate as they are all on independent channels. So if you have a second drive on the same cable as your system drive, it "might" not spin down (dont quote me on that one) because of the access to the system disk. And if you have 2 drives on a pata cable then you will have to wait for both to spin up to access one of them..
On a side note, dont expect to use any sort of monitoring utility when you set them to spin down. Cause they wont. I used SpeedFan for a while then realized my drives wernt spinning down...
And dont expect your operating system drive to spin down either... ofcourse you knew that..