The question is unclear, as other monks have noted. Let me have a crack at it. I believe you are lumping many different issues (questions) in one.

Issue 1: What if my webserver doesn't allow me to keep .cgi files wherever I want, but restricts it to cgi-bin?

Solution: In your web-server, turn on ExecCGI for the director(y|ies) where you want to keep your cgi files. In Apache, this would mean turning on ExecCGI in the httpd.conf. In IIS, you would use its management console.

Issue 2: Your CMS doesn't like you generating templates with perl (I can't really interpret your question any other way). It wants old fashioned html. Fair enough. Well, then give it old fashioned html. Of course, how on earth (and what on earth) does your CMS then generate if gets old fashioned html to begin with? The whole point of a CMS is to generate old fashioned html, not to give it old fashioned html.

Solution: perhaps you are referring to the extension, and not the type of file. Well, use mod_rewrite or something equivalent to change your file extensions. Or simply use different kinds of extensions (I believe HTML::Template doesn't care, however, other programs might get confused).