Configuration is where you configure Zen Cart.  Clear?  Well, not really because all sorts of configuration seems to happen everywhere!  This is, however, where the bulk of the setup type work is done.

These settings are all stored in the database and only are used when called. Nearly verything else in admin tends to be more active, creating lists andreports or making changes to content or working with the store itself in some way.

Some of the configurations are simply default and some, like under My Store and E-Mail Options, are set up when Zen Cart is installed:

Layout Settings is one of the more important places for design and layout work though not the only one.  If you aren't sure where to start looking, it's always the first choice.

Customer Details controls the sign up / create account form and there are also items of note underneath Shipping/Packaging that has settings that need to be tended to at first if you are going to ship with real-time solutions such as UPS or USPS.