I'm upgrading from windows 8.1 to windows 10 and I'm just wondering when sellecting this option http://i.imgur.com/fGxN0YS.png will it delete everything including all my movies and games off of my 2nd hard drive http://i.imgur.com/OlI7QCP.png
I don't think it should, because that HDD has nothing to do with Windows.
You could still take it off for safety reasons, if it's a hard drive and not a partition.