Drupal’s block system is far from ideal. It was designed back in the threecolumn-era, was improved to work beyond three-columns-content-in-middle layouts, but is still unsuited for more complex layouts.
If you want real complex layouts, you will have to turn to Panels, or Panels2. Or so they say.
A client of mine, a large Dutch media company uses Drupal for all its new sites -about four, five each month-, and untill today used panels in these sites.