Si.

Un esempio:

La tua pagina:

codice:
<?xml version="1.0"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="it" lang="it">
<head>
<title></title>
<style type="text/css">
@import url("stile.css");
</style>
</head>

<body>
<div id="contenitore">
	<div id="contenuti">
	sdasdasdasdasdsdasdasdasdasdsdasdasdasdasdsdasdasdasdasdsdasdasdasdasd
sdasdasdasdasdvsdasdasdasdasdsdasdasdasdasdsdasdasdasdasd
sdasdasdasdasdsdasdasdasdasd
sdasdasdasdasdsdasdasdasdasdsdasdasdasdasdsdasdasdasdasd
sdasdasdasdasdsdasdasdasdasd
sdasdasdasdasdsdasdasdasdasdsdasdasdasdasd
sdasdasdasdasdsdasdasdasdasd
sdasdasdasdasdsdasdasdasdasd
sdasdasdasdasdsdasdasdasdasdv
	</div>
	<script src="swf.js" type="text/javascript"></script>
</div>
</html>
Il tuo file .js che carica il flash ed evita l'attivazione in IE:

codice:
document.write('<object type="application/x-shockwave-flash" data="background.swf" width="500" height="250">'); 
document.write('<param name="movie" value="background.swf" />');
document.write('<param name="wmode" value="transparent" />');
document.write('</object>');
Il tuo file CSS:

codice:
#contenitore{
	position: relative;
	width: 500px;
	height: 250px;
	border: 1px solid red
}
#contenuti{
	position: absolute;
	z-index: 5
}