Theming Using Panel & Mini Panel

[ I apologize this is a cross-post from http://groups.drupal.org/node/39372 ]

I am trying to customize acquia slate. What is the best way to achieve a desired design? I really know nothing about designing (except for few fundamental concepts).

I am trying to accomplish this: http://gomockingbird.com/mockingbird/index.html?project=af22e4a4a6e062a2...

Can this be done with Panel & Mini Panels alone? If not how difficult it is to customize the template? Do I really need to go down the base code of the template and do the dirty stuff?

I already decided I want the Acquia Slate Theme. I am doing this for our Church as a volunteer, unpaid job. Anyone willing to extend some help?