Its quite easy actually.
Just design a site as you normally would, but while using CSS keep in mind the classes and ids that Joomla generates by default.
If you know PHP, you can edit the com_content (components) and the joomla.php (includes) to generate content like you want it, i can tell you fron expirience that editing the core files is a pain, but once you're done, everything's looking better

Then after you create the general template, for the main body section, place this in your template
CODE
<?php mosMainBody(); ?>
and for the other module positions just place this code:
CODE
<?php mosLoadModules ('ModulePositionName'); ?>
And you can add your own custom module positions by going to:
Site >> Template Manager >> Module positions
Just play around with the original template and you'll figure it out soon

Hope this helped!
Paul
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