I always start by doing the design in Photoshop, and coding one HTML page (with corresponding CSS file) in Dreamweaver, by hand in the code editor. I then take that one HTML file (usually something like 'layout.html') and split it up into a header/footer that I include on each page with PHP, or a template file for use with my framework.
For Smaller Websites (with no database needed)
I use a standard PHP header/footer setup, but with a little difference. I actually include 3 files instead of just 2. I first include a 'config.php' which sets up and defines all the variables I'm going to need (like the include path, HTTP path, timezone, etc.). I then give a little space to define custom page-specific variables that have been pre-defined in the config file (like page title, meta keywords, meta description, layout options, etc.), and include the header after that. I include the content in the middle, and then include the footer.
It winds up looking something like this:
$pageTitle = "Computer Services Contact";
$metaKeywords = "keyword1, keyword2";
$metaDescription = "We provide some super-duper awesome computer services! Come check us out!";
include(SITE_INC . 'header.inc.php');
<h2>By Mail or Phone</h2>
ABC Company<br />
1 Special Way<br />
Specialville, CA 99999
<strong>Support Line:</strong><br />
555-555-1111 (Mon-Fri 8:00am – 5pm)
<p>Do you need to <a href="<?php echo SITE_URL; ?>support/">file a support request</a>?</p>
include(SITE_INC . 'footer.inc.php');
For Larger Websites (with database connectivity)
I copy over the default 'skeleton' of my framework (I usually have to grab the updated core files from SVN because I constantly update it and make improvements), and then turn the 'layout.html' file into a template file that the main content will be placed into. I then go into setting up the database, and editing a bunch of controllers, models, etc. for all the database functionality.