I found a few links regarding hdparm/HDD tuning. One common factor is AS, so hopefully he can come and share his intelligence on this subject.

I have 3 hard drives, one for windows, one for PCLOS and one for storage (all internal).
It would be nice if I could get two of them to spin down as they are not called on too much.
The suggestion may depends on what you what to achieve. Save energy ? Reduce heating ? Reduce acoustic noise ?
Also, as I wrote in the quoted threads, depend on disks ... (Brand/model, ATA compliance ...).
http://www.serialata.org/documents/SATA_Power_Management_article_final_04_08_2009.pdfThe ATA8-ACS standard describes four modes of power consumption for SATA products
1. Active – The device is fully powered up and ready to send/receive data.
2. Idle – The device is capable of responding to commands but the device may take longer to
complete commands than when in the Active mode. Power consumption of the device in this
state is lower than that of Active mode. If a hard drive is present, it is spun up.
3. Standby – The device is capable of responding to commands but the device may take longer (up
to 30 seconds) to complete commands than in the Idle mode. Power consumption is reduced
from that of Idle mode. If a hard drive is present, it is spun down.
4. Sleep – This is the lowest power mode. The device interface is typically inactive and, if a hard
drive is present, the drive is spun down. The device will exit the Sleep mode only after receiving a
reset. Wake up time can be as long as 30 seconds.
This is a starting point, to understand what options the disk provide or not.
You need also to consider the OS settings: a journal filesystem like ext4 per default sync every 5 seconds, you need to tweak your system either by changing timings, or unmount the disk partitions if unused, otherwise the "spin down" will last at next disk access ... within 5 seconds.
I suppose you could unmount the "windows drive", but what about the "storage" disk ?
Is it OK for you to unmount the storage disk too, and manually mount it when needed ?
AS