How to layout the theme within the regions?
You cannot make region within region. You can place block in a region.
Fix the width of block and float that. You have to use only css to achieve that.

Print wrapper like this

&lt;header&gt;
&lt;?php if($page['header1'] || $page['header2']) :?&gt;
    &lt;div class="region region-header"&gt;
    &lt;?php if($page['header1'] ) :?&gt;
        &lt;div id="header1"&gt;    
        &lt;?php print render($page['header1']); ?&gt;
        &lt;/div&gt;
    &lt;?php endif;?&gt;
    &lt;?php if($page['header2'] ) :?&gt;
        &lt;div id="header2"&gt;    
        &lt;?php print render($page['header2']); ?&gt;
        &lt;/div&gt;  
    &lt;?php endif;?&gt;
    &lt;/div&gt;
&lt;?php endif;?&gt;
&lt;/header&gt;