Where do I change the content of the auto-generated store emails (i.e. customer registration, order confirmation, tell-a-friend, etc)?

The auto-generated store emails can be completed configured through the web-based admin system under the 'EMAILS' section.
To access, either click on the 'EMAILS' tab on the top nav bar or click on Store Setup and then click 'Email Messages & Auto-Generated Responses Configuration & Content' under the Email Configuration Setup section of the page.

Email content such as Subject Line, FROM Address, email greeting, message body, signature and copyright can be controlled by editing an email profile. You can also upload header and footer images to brand your emails to match your website design.

If would like to receive automatic email notifications of new orders, enter the email address that you would like to receive notifications in the BCC field of the ORDER CONFIRMATION email profile. Note: You can only enter in one email address in the BCC field. if you require multiple notification emails (BCC addresses), simply create a new email account or alias on your hosting account and enter that account or alias as the one BCC email. You may then setup mutiple forwarding addresses from the email account or alias to distribute notifications to multiple individuals.

To configure the ORDER DETAILS display in the ORDER confirmation message ( ie. purchased items from shopping cart) , click on Store Setup and then click 'Order Details Content in Auto-Generated Order Messages' under the Email Configuration Setup section of the page. This form will allow you to specify what fields such as color, size, material, sales tax, discounts, etc should be included on the auto-generated ORDER confirmation message.