Your question is somewhat confusing, but here goes anyway..

In your HTML doc (the one that's returned by the script maybe) use..
<link rel="stylesheet" type="text/css" href="/style.css">
<img src="/images/img.gif">
<a href="/cgi-bin/script.cgi">

The starting '/' will begin the path in the 'htdocs' directory

Within your script, you should use the full path to get to your .tmpl file
My guess is that you need more than "/apache/cgi-bin/application/".

Probably something like this..
"/usr/local/apache/cgi-bin/application/thetemplatefile.tmpl"