It's not a one size fits all answer. Someone would have to see the website and the files that make up the header to be able to tell you what you need to do. It's not something that can be easily answered in a forum post, especially if you have no HTML knowledge.
you just need to set id <div> tag in your css file for your flash file (width & height size etc..) and then embed the flash object code in your header.php like example below, its work for me.... <div id="flashbanner"> <object classid="clsid27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0" width="123" height="75" title=""> <param name="movie" value="http://www.domain/your-flash-file-location.swf" /> <param name="quality" value="high" /> <embed src="http://www.domain/your-flash-file-location.swf" quality="high" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" width="123" height="75"></embed> </object> </div>
The top admin bar in 3.1 is only visible to the logged in admin. Installing anything in it won't do your readers any good.