Unfortunately you cannot control drive spin-up and spin-down individually in Windows.
The drive power saving features are an all-or-nothing setting that affects all drives.
When Windows enumerates the system drives (which is a common procedure) it will spin up all the drives to ensure they are available.
One way to avoid this particular reason the drives spin up is to unmount the drives from Windows when you're not going to be using them. This can be accomplished by removing the assigned drive letter(s) from all partitions on a physical drive.
See Windows Help: Mount or dismount a drive (windows 7 instructions):
Open Computer Management by clicking the Start button, clicking Control Panel, clicking System and Security, clicking Administrative Tools, and then double-clicking Computer Management.
On the left, under Storage, click Disk Management.
Right-click the mounted drive that you want to remove, and then click Change Drive Letter and Paths.
Click Remove, and then click Yes.
For some command-line/scripting alternatives perhaps check out these SU questions: