I was installing Windows 7 on a Dell Precision laptop for my CyberPatriot team to compete with, and I threw an SSD in for extra speed. I planned to install Windows to the SSD (as the C:\ drive) and then use the mechanical hard drive just for storage. This did not work out like I wanted, as I left both drives plugged in during the install and Windows spread out the operating system across both, so that 90% of everything runs on the SSD, but due to the "System Reserved" partition, the laptop seems to require both drives to boot.
In the future, don't install Windows. :P
If you have to install Windows, just be sure to remove drives you don't want it to fiddle with.