When I do it (which is rarely, and most probably can be done much easier/quicker), I;
Open up header.php
Paste in the CSS (using link rel)
Manually 'extract' the different parts of the header (header, mainmenu, smenu area, endpage - The functions. I don't have the file at hand, so I can tell you the exact names)
Via trial and error, I paste in parts of the template, and re-integrate the PHP back into the HTML template that I just pasted in
I don't do it on a live site, for obvious reasons.
I haven't done it for a while, so I'm probably missing something, but hopefully that gives you a heads up.
Also, think about it logically when you're doing it ;)