Exactly. OS goes on the SSD. Personal files, game files, pictures, music, anything you don't want to or can't afford to lose if the OS becomes corrupted or infected, goes on the HDD. AND, you probably REALLY ought to think about an additional drive, either another internal or an external drive, to back up everything on so that if one of those drives fails, you don't lose all your crap.
At the VERY least, get some kind of cloud backup space to keep a copy of stuff you cannot afford to lose.
You can use the Windows installer OR something like Gparted to remove all the existing partitions on the current drives and install everything fresh as outlined here:
http://www.tomshardware.com/faq/id-3567655/clean-installation-windows.html
And...