When an Order is confirmed online, an email confirming the Order is automatically sent to the Contact who placed the Order.

If you ARE NOT using a Multi-Sites account, the emails are always sent from the email address which is set up in:

Setup > Organization > Account

If you ARE using a Multi-Sites account, the emails are sent from the specific email address for each Site. You can review the email address for each Site in:

Setup > Organization > Multiple Sites

Please note that Invoices are not automatically emailed from the same address but will be emailed from the address setup here: 

Setup > Organization > Invoice

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