This is a little late, but I had to figure out the other part of this question on my own and thought I would share.
To create a default menu and place it into a theme location, you will need a pre-existing location in the theme, and you will need to ensure any pages you link in your menu are also created already.
In your theme's function.php, register any menu locations. I registered two:
function my_register_navs() {
register_nav_menus(
array( 'header-menu' => __( 'Header Menu' )
, 'footer-menu' => __( 'Footer Menu' ) )
);
}
add_action( 'init', 'my_register_navs' );
Next, you will need to create your menus on site creation. I didn't use a hook for this, but instead called wpmu_create_blog manually, but you could hook into wpmu_new_blog if you preferred.
// Create the menus
$hdr_menu = array(
'menu-name' => 'Header Menu'
, 'description' => 'The primary navigation menu for this website'
);
$header_menu = wp_update_nav_menu_object( 0, $hdr_menu );
$ftr_menu = array(
'menu-name' => 'Footer Menu'
, 'description' => 'The menu that appears at the bottom of most pages in this website'
);
$footer_menu = wp_update_nav_menu_object( 0, $ftr_menu );
// Set the menus to appear in the proper theme locations
$locations = get_theme_mod('nav_menu_locations');
$locations['header-menu'] = $header_menu;
$locations['footer-menu'] = $footer_menu;
set_theme_mod('nav_menu_locations', $locations);
Lastly, you'll need to add items to the menus. Repeat this code for each item in each menu.
// Build menu item
$menu_item = array(
'menu-item-object-id' => $page_id
, 'menu-item-parent-id' => 0
, 'menu-item-position' => $menu_order
, 'menu-item-object' => 'page'
, 'menu-item-type' => 'post_type'
, 'menu-item-status' => 'publish'
, 'menu-item-title' => $label
);
// Add to nav menu
wp_update_nav_menu_item( $header_menu, 0, $menu_item );
Hope this helps! Here are some external references for you: