going to have to use a text editor.
the left column is labeled left-bar
the right column is labeled right-bar
you can more the different sections around by editing this.
<div id="left-bar">
{if $categories && ($active_modules.Fancy_Categories || $config.General.root_categories eq "Y" || $subcategories)}
{include file="customer/categories.tpl" }
{/if}
{if $active_modules.Bestsellers}
{include file="modules/Bestsellers/menu_bestsellers.tpl" }
{/if}
{if $active_modules.Manufacturers ne "" and $config.Manufacturers.manufacturers_menu eq "Y"}
{include file="modules/Manufacturers/menu_manufacturers.tpl" }
{/if}
{include file="customer/special.tpl"}
{if $active_modules.Survey && $menu_surveys}
{foreach from=$menu_surveys item=menu_survey}
{include file="modules/Survey/menu_survey.tpl"}
{/foreach}
{/if}
{include file="customer/help/menu.tpl"}
</div>
<div id="right-bar">
{if $active_modules.SnS_connector}
{include file="modules/SnS_connector/button.tpl"}
{/if}
{if $active_modules.Feature_Comparison && $comparison_products ne ''}
{include file="modules/Feature_Comparison/product_list.tpl" }
{/if}
{include file="customer/menu_cart.tpl" }
{if $login eq "" }
{include file="customer/auth.tpl" }
{else}
{include file="customer/authbox.tpl" }
{/if}
{include file="customer/news.tpl" }
{if $active_modules.XAffiliate && $config.XAffiliate.partner_register eq 'Y'}
{include file="partner/menu_affiliate.tpl" }
{/if}
{if $active_modules.Interneka}
{include file="modules/Interneka/menu_interneka.tpl" }
{/if}
{include file="poweredby.tpl" }
</div>