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