You will need code in your functions.php file that registers two (2) widget zones, with something such as this:
if ( function_exists('register_sidebar') )
register_sidebars(2,array(
'before_widget' => '<div class="widget">',
'after_widget' => '</div><!--/widget-->',
'before_title' => '<h2>',
'after_title' => '</h2>',
));
Then you can set each widget zone separately, with code such as the following:
- for widget zone 1:
<?php if (function_exists('dynamic_sidebar') && dynamic_sidebar(1) ) : else : ?>
...
<?php endif; ?>
... and similar for widget zone 2:
<?php if (function_exists('dynamic_sidebar') && dynamic_sidebar(2) ) : else : ?>
...
<?php endif; ?>
Hope that gets you pointed in the right direction ...