I have seen other themes that just define regions and then use drupals theme() function in the page.tpl.php to print the Main menu wherever the developer pleases.
This was not the case for me, and I spent a lot of time figuring out that for some reason I had to both add 'features[] = main_menu' into the theme .info file, as well as going to 'admin/appearance/settings/themename' and enable the feature before it will display.
I'm having trouble understanding why this is the case, and hope someone can elucidate or at least point me towards some enlightening documentation. Thanks.