Especially when using a fast SSD as the main harddisk, it makes sense to spin down a secondary (larger) harddisk which is seldom used.
First of all you have to know which drive is mapped to the /dev directory. E.g. you can use the program gparted to show you the relevant /dev drive.
To spin down a hard disk into standby mode use this command in the terminal application (in this case the drive is “sdb”):
sudo hdparm -y /dev/sdb
To start your computer with the secondary drive in standby mode just add the described command to the file /etc/rc.local.
In that file you can also define an automatic spin down time – e.g.
hdparm -S 120 /dev/sdb
The parameter 120 is nonlinear, so experiment with the number until it fits your needs.