Integration Method

The most important setting in your store is the Integration Method in the Store Manager section. To get to this option click on "Store Manager" from the left navigation and you will see an option called Integration Method.
 
With this option you have two choices:
Link to template Method
Integrate with Site Method
(Click on the above links to learn about these options. Please read and understand both options because this is the most important option when setting up your estore)