Make a swf file available in your template.

So there is a flash file used in the sites template, ie. on every page. This is a very simple example to illustrate method. You can see that width, height are based on the flash file, usually we force this to be exact for a template since it will often line up with non-flash elements. Also, a background color is set.

In your _phptemplate_variables section of your template.php, add this in side the case 'page': switch.

function  _phptemplate_variables($hook, $vars) {
   switch($hook) {
     case 'page' :
         $vars['swf_logo'] = swf(
    "http://example.com/files/banner.swf",
    array('width' => '420', 'height' => '140', 'bgcolor' => '#336699'), FALSE,
    array('html_alt' => '<h1>Name of site if flash is disabled.</h1>')
  );
        break;
   }
   return $vars;
}

Then in the page.tpl.php:
print $swf_logo
at the appropriate spot.