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many ways to do this. if you place that js in an actual file within your theme/js directory then you can probably call it via page.xml with
<action method="addItem"><type>skinJs</type><name>filename.js</name></action>
or you could place it directly within head.phtml and to supply the url, you could use
<script type="text/javascript"> ... swfobject.embedSWF("<?=$this->getSkinUrl('flash/faculty_sidebar.swf')?>", "myAlternativeContent", "191", "320", "9.0.0", false, flashvars, params, attributes); ... </script>
(assuming you created a /flash directory within /skin/your_interface/your_theme/)
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