I do not need it to be similar to the PHP way of embedding in HTML. It does get pretty messy that way.

In the Perl world, the mantra is There is more than one way to do it. This often leaves newbies in the position of having to make difficult decisions. To avoid embedding code in the PHP style, you may want to start out with CGI::Application and HTML::Template. There are tutorials on this site will help you: A Tutorial for CGI::Application, HTML::Template Tutorial and Using HTML::Template. As you gain experience, you may want to look at other options, but you can do a lot with these modules.