When you installed the script you probably noticed the templates directory and all the files in it. Almost all the HTML the script outputs can be found in those files. They are conveniently named: the search results template is search_results.html, etc.
You have to edit the templates on your computer and then upload them to the templates folder.
If you go to edit a template, it will look like a normal HTML file except that there are some tags that look like <#tag> floating around. Those are placeholders for data. The script takes a template file, replaces those tags with data, and then prints it to the browser. I hope that makes sense.
There are tons of tags you can use in different templates. For more on that go to the Template Tags
use a WYSIWYG editor like Frontpage to edit the templates. They get confused by the special tags and mess them up.