I have a 120GB SSD for my OS and apps and everything else goes onto traditional HDD.

Go CentOS for the operating system if you can, it's one of the 'official' linux distributions supported by AutoDesk.

You could use OpenSuse or Fedora as well if you want as they are both RPM based distros. I believe CentOS 7.1.

Skylake is fine, don't worry about overclocking for now, you want stability over speed.

I would stick with Asus, MSI or Gigabyte for a m/board.