When you reach the limits of what Drupal alone allows you to do with it's layouts, adding Panels to your site enables you to create more sophisticated displays of your content.
The command line is a powerful tool to have in your toolbox, and it's not as scary as you think! This series walks through basic command line usage, and works you up to using things vim.
The Drupal Ladder is a community initiative to get more people involved with Drupal core. It breaks the whole process down into manageable steps on a ladder. Once you complete the first step, you can achieve the next step, etc.