How to theme main menu in three columns
For a quick non-programmatic solution, you can consider using the Menu blocks module to render 2nd level menu items in 6 separate blocks, then render the blocks in the regions you want. On top of this you can also add customer classes on menu items with Menu attributes module.
If you don't mind a javascript approach, you can manipulate dom to move the sub menus around.
If you are familiar with the theme layer, you can create your custom theme function for main menu by implementing themename_links__system_main_menu.