In terms of a real-world example of what goes in these 4 different layers, assume we are writing a database-backed application that needs to fetch a user record containing various fields. This is a very common thing to do in a web app. Our template layer might look something like this:

php.ini
auto_prepend_file = "./helpers.inc"
include_path = "/usr/local/lib/php"
Template Layer
<?title('Example Page')?>
<?greeting()?>
<h1>Heading 1</h1>
  <p>
    Page content
  </p>
<h1>Heading 2</h1>
  <p>
    Yada Yada
  </p>
<h1>Heading 3</h1>
  <p>
    Page content
  </p>
<?footer()?>
Template Helpers
<?php
  include "logic.inc";
  echo '<?xml version="1.0" encoding="UTF-8"?>';
?>
<!DOCTYPE html 
  PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" 
      xml:lang="en" lang="en">
<?php
  $user = get_user_record($_COOKIE['user_id']);
  function greeting() {
    global $user;
    echo "Hi " .$user['first_name'] ."!<br />\n";
    if($age=birthday($user)) {
      echo "Congratulations, today is your ";
      echo "$age birthday!<br />\n";
    }
  } 
  function title($title) {
    echo "<head><title>$title</title></head>\n";
    echo "<body>\n";
  }
  function footer() {
    echo "</body>\n</html>";
  }
?>
Business Logic
<?php
  function get_user_record($id) {
    mysql_connect('localhost');
    mysql_select_db('users');
    $res = mysql_query("select * from users where id='$id'");
    if(!$res) echo mysql_error();
    else $row = mysql_fetch_array($res);
    return $row;
  }
  function birthday($user) {
    if(strftime('%m %d')==strftime('%m %d',$user['bday'])) 
      $age = strftime('%Y') - strftime('%Y',$user['bday']);
      if(($age%100)>10 && ($age%100)<20) $ap='th';
      else switch($age%10) {
        case 1: $ap = 'st'; break;
        case 2: $ap = 'nd'; break;
        case 3: $ap = 'rd'; break;
        default:  $ap = 'th'; break; 
      }
      return $age.$ap;
    else 
      return false;
  }
?>
In this case the final layer written in C contains the mysql_* functions, and the date() function. These happen to be standard PHP functions. If birthday() is called many times on every single request and since how you figure out if it is someone's birthday is unlikely to change very often, this may be a good candidate to translate into C. Although, in this example, the birthday function is probably too simple to see much of a performance improvement.