You can add the JavaScript on the theme level. You added on template.php or any other template that you wish to appear the javascript.
An example is a little bit tricky because is all depend on how the theme is was created. But I can provide an example base on my theme.
I'm using a sub-theme base on Boostrap so on my page.tpl.php I would add the JS on the bottom. So your goal would be to find the footer region and add the JS below that.
<?php
?>
<header id="navbar" role="banner" class="<?php print $navbar_classes; ?>">
<div class="container">
<div class="col-md-3">
</div>
<div class="navbar-header">
<?php if ($logo): ?>
<a class="logo navbar-btn pull-left" href="<?php print $front_page; ?>" title="<?php print t('Home'); ?>">
<img src="<?php print $logo; ?>" alt="<?php print t('Home'); ?>" />
</a>
<?php endif; ?>
<?php if (!empty($site_name)): ?>
<a class="name navbar-brand" href="<?php print $front_page; ?>" title="<?php print t('Home'); ?>"><?php print $site_name; ?></a>
<?php endif; ?>
<!-- .btn-navbar is used as the toggle for collapsed navbar content -->
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
</div>
<?php if (!empty($primary_nav) || !empty($secondary_nav) || !empty($page['navigation'])): ?>
<div class="navbar-collapse collapse">
<nav role="navigation">
<?php if (!empty($primary_nav)): ?>
<?php print render($primary_nav); ?>
<?php endif; ?>
<?php if (!empty($secondary_nav)): ?>
<?php print render($secondary_nav); ?>
<?php endif; ?>
<?php if (!empty($page['navigation'])): ?>
<?php print render($page['navigation']); ?>
<?php endif; ?>
</nav>
</div>
<?php endif; ?>
</div>
</header>
<?php if ($page['Featured']): ?>
<div class="BannerColor">
<?php print render ($page['Featured']); ?>
</div> <!-- /. Featured -->
<?php endif; ?>
<div class="main-container container">
<header role="banner" id="page-header">
<?php if (!empty($site_slogan)): ?>
<p class="lead"><?php print $site_slogan; ?></p>
<?php endif; ?>
<?php print render($page['header']); ?>
</header> <!-- /#page-header -->
<div class="row">
<?php if (!empty($page['sidebar_first'])): ?>
<aside class="col-sm-3" role="complementary">
<?php print render($page['sidebar_first']); ?>
</aside> <!-- /#sidebar-first -->
<?php endif; ?>
<section<?php print $content_column_class; ?>>
<?php if (!empty($page['highlighted'])): ?>
<div class="highlighted jumbotron"><?php print render($page['highlighted']); ?></div>
<?php endif; ?>
<?php if (!empty($breadcrumb)): print $breadcrumb; endif;?>
<a id="main-content"></a>
<?php print render($title_prefix); ?>
<?php if (!empty($title)): ?>
<h1 class="page-header"><?php print $title; ?></h1>
<?php endif; ?>
<?php print render($title_suffix); ?>
<?php print $messages; ?>
<?php if (!empty($tabs)): ?>
<?php print render($tabs); ?>
<?php endif; ?>
<?php if (!empty($page['help'])): ?>
<?php print render($page['help']); ?>
<?php endif; ?>
<?php if (!empty($action_links)): ?>
<ul class="action-links"><?php print render($action_links); ?></ul>
<?php endif; ?>
<?php print render($page['content']); ?>
</section>
<?php if (!empty($page['sidebar_second'])): ?>
<aside class="col-sm-3" role="complementary">
<?php print render($page['sidebar_second']); ?>
</aside> <!-- /#sidebar-second -->
<?php endif; ?>
</div>
</div>
<footer class="footer container">
<?php print render($page['footer']); ?>
/**
Load Custom JS
**/
<script type="text/javascript">llfrmid=123456</script>
<script type="text/javascript" src="https://formalyzer.com/formalyze_init.js"></script>
<script type="text/javascript" src="https://formalyzer.com/formalyze_call_secure.js"></script>
</footer>
