While working on a site I started using a javascript function called Thickbox to create attractive popup boxes. Along with the attractive popup boxes, flash was used throughout the the site. One thing Flash is well known for is being on top of everything (literally). When any Ajax or DHTML popups appeared, Flash appeared directly on top of it. The quickest and simplest solution is to give Flash a transparent background!
<param name="wmode" value="transparent" />
<embed src="file.swf" wmode="transparent" />
This makes the two play nicely together. You get what you’ve always wanted – Flash in the background over code!