I was asked this question again today on one of my videos tutorials for BB so thought that I should attempt to clarify. Although this was asked specifically about the Dynamik Website Builder child theme for the Genesis framework, it applies to virtually all themes.
Note that I did not want to ‘confuse’ the issue with BB’s new-found functionality of shortcodes as of 1.7; that’s for another post 
The difference between BB and your theme
Cheers!
Lyle