Just the main script goes in the header.
This part:
<script type="text/javascript">
swfobject.registerObject("myFlashContent", "9.0.0");
</script>
should go at the bottom of your html module content after the actual object with the id "myFlashContent"
The scriptloader will include the main swfobect script in the page for you if you set the property I mentioned.
If your layout.master does not have the ScriptLoader then copy it from another skin.
Hope it helps,
Joe