Dear estreetz !
You can do it following way below :
Open index.php file in templates/ja_xenia_ii folder, find following code section at about line 93 :
<img src="<?php echo $tmpTools->templateurl();?>/images/logo-<?php echo $tmpTools->getParam(JA_TOOL_COLOR); ?>.jpg" alt="<?php echo $tmpTools->sitename(); ?>" />
replace it by code for load flash file.
example about code to load flash :
<object height="278" width="900" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=9,0,28,0" classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000">
<param value="[path to flash file]" name="movie"/>
<param value="high" name="quality"/>
<param value="opaque" name="WMODE"/>
<embed height="278" width="900" wmode="opaque" type="application/x-shockwave-flash" pluginspage="http://www.adobe.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash" quality="high" src="[path to flash file]"/>
</object>