Hi localdog
terrific.js should not be that confusing. If you already read the concept behind at
http://terrifically.org/ – it's all about modularizing your javascript code based on your .mod css classes – everything you need look for in your purchased theme is where the modules are located. I don't know about your theme, but my guess is, that there is one javascript file per module.
So all you need to know is, that the javascript file in your module – especially the 'on' hook method – is executed if the module (class .mod-xyz) is present on your current page.
For all the other questions please contact the in-depth documentation at
http://terrifically.org/api/ – especially the modules and bootstrap chapter – or feel free to ask again :-)
Hope this helps & Cheers
Remo
btw: Which theme are you using?