In some cases, you may desire to use panels as the primary layout tool for your website.

Update: This tutorial is redundant especially for new projects. Panels 3 replaces Panels 2, and the module Panels Everywhere provides the same mechanism as this tutorial.

Why all panels?
A typical situation is where you are leaning on panels heavily to override nodes, suppressing blocks/regions on panels pages, and perhaps have a panels_page as a front page. You're at the stage where themer has developed page.tpl.php and css that matches the design specs, and the site looks hot.

Now, go to a page that is not a panel, like node/add, and you realize that the work has just begun for pages with the traditional sidebar_left, sidebar_right mentality - you have all the extra printing in your page.tpl.php, or you need to have a separate page.tpl.php for panels and non-panels. Wouldn't it be easier to just have everything as a panel? You'd be practically finished.

Why not % override?
The obvious option is to create a panels_page with the path '%' to be the default path override. However, the result is a panels page missing the original content. This is because when Panels overrides the menu path, it obliterates any previous callback information with it's own. In the case of node pages, this is ok, Panels figures out the context and calmly renders the node data. But this requires specific code for each context.

A great thing about Drupal 6, is that it will be possible for Panels to use the new hook_menu_alter() to store the callback information about the page it is overriding. So on node/add (for example), panels will know to call node_add() for the $content. This is not possible in Drupal 5. Update: Panels 2 can do node/add, but I'll use this example for simplicity - see here.

Steps to override any page with a panel
If you are happy to configure things on a site by site basis, the steps to achieve this are pretty straight-forward:

1. Go into block configuration admin/build/block and create a new block. Call it CONTENT, and in the body type %CONTENT%. Make the block PHP format to avoid additional markup when it is displayed.
2. Go into your Panels admin, and add a new Panels Page. Call it DEFAULT, add whatever content you desire, but in one of the areas, add the block you created in the previous step.
3. Now open your template.php and put this code in _phptemplate_variables(), where $op = 'page'.

   <?php
     $current_panel = panels_page_get_current();
     if (!isset($current_panel->pid)) {
       // Load our default panel, call it by name.
       $panel = panels_page_view_page('DEFAULT', false);
       // Insert the actual content of the page using string replace.
       $panel = str_replace('%CONTENT%', $vars['content'], $panel);
       // Replace the page content with our altered panel.
       $vars['content'] = $panel;
     }
   ?>
   

Extra tweaks
It may be worth considering pushing extra $vars like $messages and $help into the panel as well - more information may follow.