You can manage the inventory of your Items automatically (and manually) on your website Admin Panel.  Enter in each item's inventory on the E-Commerce > Add/Edit Item pages. 

Choose whether to update inventory automatically after a customer's purchase on the Configure Site > E-Commerce page.  You can also choose whether or not to sell an item when it is out of stock, and customize any messages to display when an item is out of stock or has a limited supply left, based on your set value for "limited supply".