Its always recommended to have only the hard drive that the installation is made to, plugged in - the reason for this is that during the Windows installation, some system files could be written to the other hard disk. You won't notice this difference until you plug that second disk out.
So, we always recommend to only have the one disk plugged in to the motherboard during installation to prevent this from happening. See this recent thread where exactly this problem occurred: Win7 No Longer Boots After Removing Spare Drive, Why?
All you need to do, is unplug the SATA cable from the HDD/HDD's until your installation is complete. Once complete, shut down the PC, reconnect the SATA cables, and then reboot the PC.