Open customer/home.tpl in a text editor (not notepad) (I suggest
www.pspad.com).
Look for <!-- main area --> Under that you will see several sections that look like this..
{if $active_modules.Manufacturers ne "" and $config.Manufacturers.manufacturers_menu eq "Y"}
{include file="modules/Manufacturers/menu_manufacturers.tpl" }
{/if}
These are your "boxes", in this case the "Manufacturers list.
Some will be enclosed in "{if}-{/if} tags, and these probably need to be included as in the example above. Others will not and simply look like
{include file="news.tpl" } in this case the "News" box.
The left column ends where it says <!-- central space -->
The right column begins where it says <!-- /central space -->
When you save your edited home.tpl, give it a new name, like home.tpl-new for example. Upload using FTP to the same folder on your site and change the name there (renaming the home.tpl that is there to home.tpl-old first.
Good luck!