The Base class is where you would ideally put the customized load_tmpl method. This way your entire project gets the benefit of the change, but other users of CGI::Application on the system will not notice a difference.
I didn't even think of overriding other CGI::Application methods. Yes, I already have a subclass of CGI::Application for the app in question, but I hadn't gotten to the point of changing any default behaviour in methods ( because, frankly, I don't know it well enough to want to jump too far into it ). But, next time around ( and if i get a chance to refactor this project ), I'll do just that: have a customized my_load_tmpl() method that acts just like load_tmpl() with a few added fun things.