Separate content and sidebar-last

Today acquia marina layout looks something like this:

Picture: http://groups.drupal.org/files/acquia_marina_layout_v1.JPG

And because sidebar-last is not clearly separated from content, some very important things go below sidebar-last.

Picture: http://groups.drupal.org/files/acquia_marina_problem_x.JPG

Many people has this problem and no one knows how to solve it. i.e. how to separate content from sidebar-last. Doing it would be great, if you need to have two sidebars: in a left to show advertisements, menus, views and other important blocks.

Picture: http://groups.drupal.org/files/acquia_marina_layout_v2.JPG

To solve this, I have been changing theme's CSS code, to make smaller sidebars, make fixed (490px) content region. To lift some things up (by changing clear:both; to clear: none; or clear:left;). But I solved only half of them, content and sidebar-last is always somehow interfering. I think, that something needs to be changed in PHP, to clearly separate these regions. Maybe somebody in this group knows how to do it?
jwolf said that this is by design, so maybe its good to create a subtheme?