So you want to include SSI directives in the output from your CGI script, but can't figure out how to do it? The short answer is "you can't." This is potentially a security liability and, more importantly, it can not be cleanly implemented under the current server API. The best workaround is for your script itself to do what the SSIs would be doing. After all, it's generating the rest of the content.
This is a feature The Apache Group hopes to add in the next major release after 1.3.