Easiest is to take a copy of Controller_Template (which is in fuel/core/controller/template.php), swap the View code in there for Theme code, and use that as a base controller for your controllers.
In the after() method, if the method called didn't return a response, you create a new response with the Theme instance as payload.
Just have your controllers extend it, set the $template property in your controllers to the desired page template, and use \Theme::instance()->set_partial() in your methods to define template partials.
Providing you've got the theme.php config correct, this should work...
Thanks for all the help Harro, I am learning more and more every moment working with Fuel.
I have the theme system working, now I just need to pass variables to my partials. I am calling $theme->set_partial('header','layouts/header')->set('title', $title); and in the partial i am calling <?php echo $title; ?>