Create a new page in wordpress theme

i am creating a functionality in word-press where i need to create a new php page and have to link it in the menu section of my website.Though i can create a page from the dashboard but due to some reasons that option has been discarded.

Aim is to create a new page and link it with my existing site.i have crated a page with following entries

<?php get_header(); ?>

    <div id="content">
        <span class="breadcrumbs"><a href="<?php echo get_option('home'); ?>/">Home</a> &raquo; Custom</span>
    <h2 class="title">Custom page</h2>
    <p align="center">
        <?php mycustomFucntion(); ?>
    </p>
    </div>
</div>
<?php get_sidebar(); ?>
<?php get_footer(); ?>

i am clueless how i can link it with my existing site so that when some one click on the link on menu user should be redirected to this page.

<ul id="page-bar" class="left clearfloat">

    <li><a href="<?php echo get_option('home'); ?>/">Home</a></li>

    <?php wp_list_pages('sort_column=menu_order&title_li='); ?>
    <li><a href="<?php echo get_option('home'); ?>/">CustomPage</a></li>
    </ul>

i am just playing around with php and word-press in J2ee i know i can hit an action class and can return this custom page as new view but not sure how i can do this in word press

any help will be much appreciated Thanks in advance