How can I set everything up so that the majority of my files are installed and accessed from my HDD while a select 'few' programs are actually on my SSD?
As you install applications, choose Custom or Advanced. Then you can choose where each one goes.
However, for a 256GB drive, you should have zero space problems with applications.
I have a 128 as my boot drive, and everything except Steam, MS Office, and the virtual machine drives installed on it. Win 8 Pro + Media Center, Lightroom, and older version of Photoshop, PaintShopPro, LibreOffice, a zillion utilities.
Current use is ~65GB.
Applications outside of games don't really use that much space. Install games elsewhere, and you'll be fine.
And of course music/movies/images elsewhere.