Operating systems will be installed where you choose them to be installed to lol.
However if you are not sure where Linux OS will now be installed or you simply do not want to ruin Windows OS on the second HDD,you have 2 choices:
-Go to your BIOS and disable the HDD on which your Windows OS is installed.On this way Linux OS will have no other choice but to install on that first HDD because the second one is disabled...
-Open your computer case and unplug the HDD on which your Windows OS is installed.On this way Linux OS will have no other choice but to install on that first HDD because the second one is unplugged...
But like I said...today almost ANY operating system offers you the choice where to install it...
This of course was not the case with Windows 95,98 and ME because they could have been installed only on "C:" partition which they would create automatically and make it to be big as the entire HDD,but even then there was STILL a way to install them on other partitions then just on the "C:" partition.
Cheers!