I tend to prefer to have a separate master file that drives the entire site depending on how large they are. I generally start most of my projects as standalone CGI with the intention of porting them to mod_perl so I create a handler subroutine that is the first thing called in my applications. The handler then calls different sub-handlers depending on the mode and the submode cgi params. I have used HTML::Template for small projects but have been really considering Template Toolkit for all future projects. The code is structured around the classic Model-View-Controller pattern. See this article for a good example of this.

Good luck.