What email is shown as the "from" address on the Customer's Confirmation email that they receive?

The confirmation and notification emails will come "from" the email address that you have set up on the Settings page in the Notification Email field.  If you have multiple Locations with different emails for each Locations, you can have the system use the appropriate email for each, by setting the "Use Location Email" box to YES.  Make sure each location has a valid email address under Tools>Edit Settings>Locations