implementing javascript across the site

[DrByte]

You can load scripts in the html_header. just like you would do in any html template. Reference to the location in this file using the standard html link for css or jscript.

... and it's only necessary to do that if you have very special requirements that won't work by simply putting the required files into the prescribed folders as discussed above.
The idea behind making the folders and naming conventions available as automatic loads was to prevent you having to touch any template files when simply wanting to add javascript handling onto the page.