From Administer > Site building > Home box, click on layout link in front of one of your page.

This leads you to a form similar to Drupal standard block administration.
As you can see, by default, 3 columns are provided, they all are empty. Disabled blocks zone shows you every single blocks existing in your Drupal installation.

You can assign blocks to any column by drag/dropping a block from the disabled zone to one column of your choice. You can also achieve this by selecting any column in the drop down in front of each block.

This way you can create a default layout for your home box page.

IMPORTANT: You have to understand that this is only a default layout. As Home box is designed to let user build its own page, we are now creating the layout that the user will see the first time he or she uses the page. We hope that the user will modify its page to suit her needs (moving blocks, disabling blocks, etc.). So keep in mind, this is only the default layout.

By unchecking the Visible, Open, Movable options, you can prevent a block from being shown by default, collapsed by default or dragged to another column. Most of the time you won't need to uncheck this option.

Once you're done, you can click the Save blocks button. You can now jump to the settings section.