The cloning software is if you're moving your operating system to a new disk. So yes, you can plug it in and expect it to work, though you'll still need to install an operating system before you can really do anything other than post. I would recommend at least attempting Linux at first, but you have an NVidia card and you don't sound all that experienced. Get your hands on the Windows 10 preview and look into getting 7 or 8, since the preview won't last forever.
However, you'll want to install your OS onto the SSD, as well as any games. That will ensure the best performance. It wouldn't affect in-game performance if you installed everything on an HDD, but it would be considerably slower when loading or booting.
Havn't set it up yet, at work at the moment. My parts just arrived today as told by my girlfriend and I am Psyched to put it together when I get home. (: Thank you for the info, one more question...
What is the best looking Skyrim game you have seen? I am building this with that in mind and I am assuming the 980 STRIX OC will handle more than a handful of mods.