My first thought would be to include your flash header inside the headerWrapper.
Code:
<!-- bof flash insertion -->
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=5,0,42,0"
id="header" width="750" height="130">
<param name="movie" value="header.swf">
<param name="bgcolor" value="#FFFFFF">
<param name="quality" value="high">
<param name="allowscriptaccess" value="samedomain">
<embed type="application/x-shockwave-flash"
pluginspage="http://www.macromedia.com/go/getflashplayer"
width="750" height="130"
name="header" src="header.swf"
bgcolor="#FFFFFF" quality="high"
swLiveConnect="true" allowScriptAccess="samedomain"
></embed> </object><!-- eof flash insertion -->
<!--bof-header logo and navigation display-->
<div id="headerWrapper">
move the highlighted portion to above <!-- bof flash insertion -->