Javascript, How to Load in WordPress ?

A bit of javascript displays nicely in a php file

However it does not work when in wordpress,

Attempts Sofar:
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added include(“/art.php”) to the template wordpress files. index.php, category.php

added the javascript directly to the templates.

added the javascript to the “html” view of the wordpress gui

added the include(“/art.php”) to the “html” view of the wordpress gui with the php-exec plugin which normally allows php from the “html” view

tried all of the above making certain to insert the type and src into the head

All didn’t seem to display the javascript which seems to display all right when not integrated into wordpress.

Here could be the same issue is a post from 4 months ago:
http://wordpress.org/support/topic/217046

Alternative: loading sidebar functions from non wp pages