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What script are you using, you may need to edit more then one file the exact same way. Chances are, you index.php for the script is primarily blank, in which case look inside and look for anything that has ..include and edit the files it's references, or put your custom pages (with .php extention and above mentioned edits) in the directory it might specify in the script.
There is more then one way to do, and sometimes it's hit or miss depending on your skills. Even when things look like they should be obvious, it just doesn't work till you edit the right files through trial and error.
Let me know what script it is and I'll see if I can incorporate it into my site. If successfull, I'll report which files to edit.