Hello Rena,
Welcome to Moodle. I am also new and we have several .js menus on our site. Our site is very customized and we are considering creating separate files to embed menu links instead of dealing with designing Moodle elements. We're doing this because we don't want every item we create to show up in the menu for the header or sidebar. But for now, our horizontal header menu is located in a separate header directory that contains the .js file. The header picture is in the pix directory. Then, we placed the menu design code into the layout stylesheet (we included all features color, font, etc... for the .js file in this location). Make sure all of your links are correct and the style sheet location is placed correctly in your .js file.
Contents of header.html:
<div class="headermain"><img src="<?php echo $CFG->wwwroot.'/theme/'.current_theme() ?>/pix/home.jpg" ></div>
<div class="headermain"><script type="text/javascript" src="<?php echo $CFG->wwwroot.'/theme/'.current_theme() ?>/header/your.js"></script></div>
<div class="headermenu"><?php echo $menu ?></div></div><?php } else if ($heading) { // This is what gets printed on any other page with a heading
?><div id="header" class="clearfix">
<div class="headermain"> <img src="<?php echo $CFG->wwwroot.'/theme/'.current_theme() ?>/pix/home.jpg" ></div>
<div class="headermain"><script type="text/javascript" src="<?php echo $CFG->wwwroot.'/theme/'.current_theme() ?>/header/your.js"></script>
</div></div><?php } ?>
Here is another link on editing the header.html file: http://moodle.org/mod/forum/discuss.php?d=87562
A vertical .js file menu can also be placed in a "label" block. I would not use an html block because that only links you to an html page. Make sure your design elements and links are correct. You will do just fine.
Best Wishes...