Click on the 'Cart Reminders' link under the 'Commerce' heading in the Control Panel menu. Then, set 'Automate' to 'Yes' and choose when you'd like the reminder email sent (the default of 3 days is shown below).
Edit the subject line, intro, closing, and footer. The main body of the email will be links to the items left in the customer's cart. You can edit how these links appear under 'Book Display.' When you have finished customizing your cart reminder email, click the 'Save' button.