3
Scripts should be done just like any of the others in your site, such as:
<script type="text/j-a-v-a-s-c-r-i-p-t" src="path from web root/file.js">script>
(of course, remove the hyphens, used to prevent protector from protecting). You can do the same thing for the css, although I usually would suggest putting that into your theme's CSS.
As to the javascript in a custom block, zzzzsg, that specific issue will require some debugging. Javascript WILL run in a custom block just fine, but there is a problem with that particular code.