After some fiddling with layered divs in Drupal (and it is possible), I figured I'd post what I found out. The need for this came about when trying to convert the layout of an existing site done in html with javascript menus. The idea was to recreate without using the enormous amount of generated code in the original source and still work within the limitations of displaying mixed content in the header of each page.

Because the 'logo' in most themes is laid out in fixed terms - trying to integrate different graphics is sometimes ugly. So, I decided to layer the logo image and the navigation bar so that the navigation is fixed in the lower right section of the header. The logo image must be positioned behind the navigation bar for the links to work -AND- the header DIV must be positioned behind the nav bar DIV. The only reasonable thing then is to wrap each of these divs in container divs and assign layer ID's with cooresponding classes in the CSS with z-index attribute controlling which layer is on top and which on bottom. For the purpose of this example, I started with the nokoala theme by R Kr

-----CSS snippet----

/*use of layers to create logo and lay menu in lower right position*/

#Layer1 {
    position:relative;
    left:0px;
    top:0px;
    width:100%
    z-index:1;
}
#Layer2 {
    position:relative;
    left:0px;
    top:110px;
    z-index:2;
    }

/*end*/

Then wrap the header and nav divs in page.tpl.php:

-----PHP snippet------

<div id="Layer2">
 

<div id="nav">
  <?php print $top_menu; ?>
  </div></div>

<!--/#nav-->
 

<div id="Layer1">
 

<div id="header">
  <?php if ($logo) { ?>
  <a href="<?php print $base_path; ?>" title="<?php print $site_name.' '.t('Home Page');?>">
  <img id="logo" src="<?php print $logo; ?>" alt="<?php print $site_name.' '.t('Logo');?>" /></a>
  <?php } ?>

  <h1 id="site-name"><a href="<?php print $base_path; ?>" title="<?php print $site_name.' '.t('Home Page');?>"><?php print $site_name ?></a></h1>

  <?php if ($site_slogan) { ?><div id="site-description"><?php print $site_slogan; ?></div><?php } ?>
  <?php if ($search_box): ?><?php print $search_box ?><?php endif; ?>

</div></div>

<!--/#header-->

 -----end of snippets