Dan-

Welcome to Zen Cart! Sounds like you are figuring most things out okay. I will give you a couple of hints to help you on your way. First, the menu that is horizontal under the header is called Cat Tabs (category tab menu). I can be turned on and off in the admin in Layout settings, styling- use the stylesheet.

The sideboxes are also controlled inthe Admin> Tools> Layout Boxes Controller.

Suggest you play with some of the other gazzilion switches to see what they do too.

Enjoy!