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Three simple rules you need to know about menus:
Your best bet to control any menu in XOOPS is editing its template. Templates are grouped by module, so Main menu template belongs to "System - blocks" and the other one belongs to "AMS - blocks".
Main menu is controlled by a template in system module. The AMS menu is another template in AMS module.
To supress the "home" button just delete the home tag in main menu template.
To add stuff in Departments menu, just add it at the end of the template. Ability to read and write HTML will be useful at this point.
Submenus are defined in xoops_version.php - Every module has it's own xoops_version.php file, locate AMS's, and look for this:
['sub']
This is part of the PHP code that defines the submenus.