create a div for your flash. set div opacity, or z-index parameters.
use jquery last version and use windows load function like this
$document.ready(function () {
$("#divForFlash").animate({
"toggle": "hide", "opacity": "hide"
}, { duration: 10000 });
});
you can set your divForFlash div like this
<div id="divForFlash" style="position:absolute; width:1000px; height:620px; z-index:10x; display:block; top:-600px;">your flash code </div>
dont forget set your flash divs style like you need for your web page design
i tried to told shortly. if you didnt understand you can ask, after then i will tell you clearly more than this.