A lot of people for the first time opening up WordPress can be over come by all of the stuff that there is to a theme. I like many others, one tip I can offer is to open up your header.php footer.php and sidebar.php and insert a php comment or an html comments, making sure not to put and html comment at the top of the header page, it will cause your problems later on down the road.
what i then do after that is viewthe source code in my visually un altered WordPress theme. open up your favorite web script editor and paste the code into a blank file, i named mine index2.php and then remove all css linkes and attach the style.css file to you index2.php.
you should now have a flat non dynamic file that has the same look as your default theme. with the css file linked you can now edit the peramiters and see what is going on. assuming you want everything to work as it should you can then look for the comment lines in your index2.php file and open up the corresponding template file and fill in the blanks, it should go rather smotheley from there.
since wordpress is mainly CSS driven its a good idea to put as many comments into your CSS file so it will make sence to you later on down the road.
my CSS structuring in comments is set up like this:
Theme Name: Studio Lounge Theme URI: http://www.studiolounge.net Description: Studio Lounge Template Version: 2.0 Author: Adam Patterson Author URI: http://www.adam-patterson.com File: style.css - main site design and layout. E-mail: adam@adam-patterson.com 1) Imports - print 2) General selectors - body,h1/h3,p,input,textarea 3) link rules - default 4) Structure: A: container B.1: header B.2: navigation B.2.1: header menu C.1: content C.1.1: main posts C.1.2: meta C.1.3: comments D: footer E: sidebar 5) Style 6) Hacks