If you wish to remove your background from your Flash file when using xhtml/css (handy when integrating in your Flash into a Photoshop built layout) add the following code in your Flash object code:
<param name="wmode" value="transparent"> between the open and close object tags.
So your full object code would now look like:
<object type="application/x-shockwave-flash" data="yourFile.swf" width="550" height="400">
<param name="movie" value="yourFile.swf" />
<param name="wmode" value="transparent">
</object>