Primary, secondary links to organize website

I am redesigning my school's website and I'm looking to use Drupal. I will admit, I'm new to this CMS as well as to the navigation system that Drupal empowers. Here's the story:

1. I need to seperate the website into 6 main sites: one for each of the schools in our school district.

2. Within each school I need to have menus and submenus.

3. So I have 6 menus and 6 sites and I need to pair them up so that the menu only appears on the pages that it coinsides with. I also need to have links to the 6 different schools at the top of the page.

I suppose part of the problem is that I don't know how Drupal seperates the content and the menus from the theme...

I truly appreciate the help. If it helps I need to match the Drupal system found here (http://mickens.us/mockups/drupal) to fit this design [ultimately] (http://mickens.us/mockups/shawnee_heights)... Thanks!