Main Menu vs Navigation Menu
My personal opinion is that this is pretty subjective.

We typically just use the main menu for just top level section links (ie, all links are at the top-level and don't have children), and then will have a menu per site section.  We will also typically have a sub menu for extra header links and extra footer links.  Our theme will take care of displaying the proper menu on pages.

Keep in mind that we also do highly custom themes for large sites, so this scheme may not apply for your needs.