Thanks for the reply Jochem. Since I've built a custom checkout widget that setting is not available, but I could add it. However, since the MerchantEmail is used as the "From" address for order confirmation emails sent to the customer we've set it up as a "no-reply" address. We'd rather not send out the store managers real email address to everyone. So, it looks like I may have to create my own function to generate the email. We need it to go to multiple addresses anyway.
It might be useful for others though if Sitefinity provided the ability to specify a list of email addresses, separate from the 'reply to' address, where a copy of an order confirmation can be sent for internal merchant use.