How to place a div inside a function that creates a div

I don’t think you can use that function and do that but I do not know anything about bones_main_nav . Using the default WordPress function ( which the bones function is wrapping) will only output <ul>...menu items... </ul>, then a simple way is to just wrap it in your template file.

For example:

 $defaults = (array(
        'container' => false,                          
        'menu' => __( 'The Main Menu', 'bonestheme' ),  // nav name
        'menu_class' => 'nav top-nav clearfix',         // adding custom nav class
        'theme_location' => 'main-nav',                 // where it's located in the theme
        'before' => '',                                 // before the menu
        'after' => '',                                  // after the menu
        'link_before' => '',                            // before each link
        'link_after' => '',                             // after each link
        'depth' => 0,                                   // limit the depth of the nav
        'fallback_cb' => 'bones_main_nav_fallback'      // fallback function
        ));

And your template markup would be:

<div class="nav footer-nav clearfix">
<?php wp_nav_menu( $defaults ); ?>
<div id="menuTab"></div>**<!--THIS IS WHERE I WANT MENU TAB TO GO-->**
</div>

A more complicated way via code would be to use a Menu Walker

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