I'm making some assumptions here. Your confusion stems probably from the fact that you have little idea how the Web works on the HTTP message level. Read a book or two about modern Web development, the concepts should transfer easily to your tools of choice. Following is a very small PSGI application to get you started. The application-specific JavaScript can also be put into a stand-alone file. Yes, a templating system is a good idea. So is using a Web framework, which is a small step up from printing out HTML piecewise. 
my $app = sub {
    return [200, ['Content-Type' => 'application/xhtml+xml'], [<<'END_
+HTML']];
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
    <head>
        <script src="http://code.jquery.com/jquery-2.0.3.min.js"></scr
+ipt>
        <script>
jQuery(document).ready(function(){
    jQuery('p').append(' Hello world from jQuery!');
});
        </script>
    </head>
    <body>
        <p>Greetings.</p>
    </body>
</html>
END_HTML

};

[download]
edit: JS does not need to be in the HTML

In reply to Re: How do I mix up Perl and jQuery (for beginners) by daxim
in thread How do I mix up Perl and jQuery (for beginners) by eyekona

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.