Note: This user guide assumes that you are working with Commerce Kickstart 1.x or that you are familiar with Drupal. It's very important to get the right set of modules turned on and a number of configurations need to be setup for content types and custom entities. See Installing Drupal Commerce for more details.
Building a Drupal Commerce site is easiest when you have at least some familiarity with administering Drupal itself. With the release of Drupal 7, navigating the backend is easier than ever, but there's still quite a lot to learn. Familiarizing new users with Drupal is out of scope for this documentation, so we recommend using other freely available resources to get up and running on Drupal 7 before installing and configuring the Commerce modules.
To setup a new Drupal Commerce site, you're going to end up creating a custom content type, using Drupal 7's Fields system, and learning to navigate the complex Views and Rules modules for advanced store customization. This guide won't teach you everything there is to know about customizing Drupal Commerce, but we hope to provide at least the basics.
This user guide is for Drupal Commerce 1.x and is subject to change. Please feel free to add comments.
Another source of information is the screencast series on Commerce provided by Commerce Guys. You can subscribe there to get notifications of new screencasts...