Before you can sort out the PHP, you need a Apache/PHP/mySql setup.
You should learn how to setup a webserver on your development machine at home. Then learn on the development machine instead on a remote server.
Read the following to get started:
PHP and Apache installation
If headers, footers, menus are the same throughout your website, then you would create a PHP file containing HTML/PHP code. Here's a general idea of what it would look like:
<html>
<head><title>blah</title></head>
<body>
<div id="header">
<?php require_once("header.php"); ?>
</div>
<div id="content">
<div id="menu" style="float: left; width: 180px;">
<?php require_once("menu.php"); ?>
</div>
<div id="column" style="float: left: width: 580px;">
Your stuff here
</div>
</div>
<div id="footer">
<?php require_once("footer.php"); ?>
</div>
</body>
</html>
Header.php
<a href="http://www.mysite.com/" title="mysite">
<img src="logo.jpg" alt="my logo">
</a>
Footer.php
Copyright © mysite.com
Menu.php
<ul>
<li>Menu item #1</li>
<li>Menu item #2</li>
<li>Menu item #3</li>
<li>Menu item #4</li>
<li>Menu item #5</li>
</ul>