What I usually do is copy the folder where the default theme is located and name the folder whatever the site name is.
Then I go in that folder and start editing the header.php and style.css files so the layout starts looking the way I want.
Once you're messing around in those pages everything will start to make sense.
Oh yeah, also edit the header of the css file since you'll need that to get you own them to work...
Anyway on these pages you'll find more info:
http://codex.wordpress.org/WordPress_Lessons