This article is how you modify the menus to include a custom menu – usually replacing the top navigation menu.
http://codex.wordpress.org/Navigation_Menus
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Navigation Menus
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Navigation Menu is a theme feature introduced with Version 3.0. WordPress includes an easy to use mechanism for introducing customised navigation menus into theme. In order to incorporate menu support into your theme, you need to add a few code segments to your theme files.
Function Reference
Register Navigation Menu
register_nav_menus()
register_nav_menu()
unregister_nav_menu()
Show Navigation Menu
has_nav_menu()
wp_nav_menu()
Contents
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1 Function Reference
2 Edits to functions.php
3 Now add locations to your template files
4 Back to the Menus Panel
5 External Resources
6 Related
Edits to functions.php
Firstly, in your theme’s functions.php, you need to write a function to register the names of your menus. (This is how they will appear in the Appearance -> Menus admin screen.) As an example, this menu would appear in the “Theme Locations” box as “Header Menu”.
function register_my_menus() {
register_nav_menus(
array(‘header-menu’ => __( ‘Header Menu’ ) )
);
}
And this would make two menu options appear, header menu and extra menu -
function register_my_menus() {
register_nav_menus(
array( ‘header-menu’ => __( ‘Header Menu’ ), ‘extra-menu’ => __( ‘Extra Menu’ ))
);
}
Then you need to ensure that the theme turns these menu options on, so you need this bit of code as well -
add_action( ‘init’, ‘register_my_menus’ );
The above tells the theme to run your “register_my_menus” procedure. As you can see, your new function makes use of the WordPress register_nav_menus functionality.
Now add locations to your template files
Once you’ve done that, your theme will be almost ready. The last preparation step is to tell the theme where you want the menus to show up. You do this in the relevant theme file. So, for example, we might want our header menu to be in header.php. So open up that file in the theme editor, and decide where you want to put your menu. The code to use here is wp_nav_menu which we will need once for each menu location. So, add this code -
All you need to ensure is that the theme_location points to the name you provided for your menu in the functions.php code above. (Note that it’s the header-menu being used here rather than Header Menu without a hyphen. header-menu is the name that the code understands, Header Menu is the human-readable version that you see in the admin page.)
To complete the code, you can put your extra menu someplace else. Maybe you want a menu on one of your pages, for example, and you might even want it to be jazzed up a little with a containing DIV of a certain class -
wp_nav_menu( array( ‘theme_location’ => ‘extra-menu’, ‘container_class’ => ‘my_extra_menu_class’ ) );
So you’d put the above into your Page template, and not only would the menu show up wherever you put it, it’d be styled as my_extra_menu_class so that you can work with that in CSS.
Back to the Menus Panel
WARNING: If you do not have the Menus SubPanel under Appearance, you need to ensure your theme has add_theme_support( ‘menus’ ) in your theme’s functions.php file.
That’s all the background work. To finish, you would simply visit the Appearance -> Menus panel in your site admin. Now, instead of seeing some text suggesting that your theme doesn’t natively support menus, you’ll see some Theme Location options.
You can now use the GUI menu creator on this admin panel to put your menu(s) together. Give them each a name, and then assign a menu to a location with the pull-down options.

Keep on writing and chugingg away!
I learned a lot from this post, great help for me, thank you!
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Arron