To make it easier, uninstall the hdd and load windows with only the ssd installed in the first sata port, usually sata0. Then install the latest MB drivers and get your system setup and running right. Then install the hdd and you should have access to it to do whatever.
Correct, there are software f.eks Samsung Magician that will allow you to clone your original OS drive over to the SSD. But these softwares either commes with the purchase and will only work with that spesific brand, or you will have to buy an aftermarket software to do the job.
Seen 1 or 2 that are freeware, but they required that the SSD is the same size or larger than the HDD you are cloning. In other words, won't work for you seing as your HDD is 1TB and the SSD is 256gb.
Don't think any of the cloning softwares will allow to only clone certain files. Its either everything, or nothing.
Now just copy / paste an OS or Steam games won't work. So you might aswell just do a clean install for the games and OS on the SSD right away. Will probebly be faster than waiting and trying out 100 different other options that might or might not work. ^^