You can do quite a bit of the layout work for your website in the Panels UI.
Maybe the most controversial module in the Drupal community because I think the UI turns a lot of people off. I have scaled back on my Panel’s usage on sites in favor of context but I still like using the ‘node template’ panel for rendering the output of a node detail page and also for 1-off layouts like homepage layouts. For these use cases, Panels is very handy. http://www.mediacurrent.com/blog/jays-top-50-drupal-7-modules