Hi apljdi,
if we take the website in this link the standard layout and how I would extend it.
I am not a designer I am a software developer, so I will create the default look in Artisteer, this will produce a basic two sidebar, small footer, basic menu and no category menu website.
load the theme on my local wordpress, then from my plugin, the first form is management, I enter the sheet width and details of the two sidebars, then extend enter names for the other two sidebars and the width, options for 5 full 100% width content areas, two 50% and one 33%, then the dynamic footer bars 4 widgets areas.
Next screen generates a css file based on the management details, this will not happen unless the information is correct, copy the css text, go to admin > themes and edit, the plugin comes with a folder and four files that go in your theme folder, from the editor open up drflayout.css and paste in the css text.
next screen is where you choose the elements to generate a template, so for the home page I may add content panes 1 to 5, and any combinations of sidebars there are 15 different sidebar layouts,that you can add differen content panes to, this screen also generates the template code, copy paste and save the template, repeat as many times as you want with different combinations.
david (phew!)