If you are using the text email receipt, you can add custom text to the bottom of the receipt in the backoffice under:
Commerce Setup -> Order System -> Thank You
"Text at the bottom of the email receipt:"
You can also change much of the text at:
Preferences -> Store Text -> Receipts
If you are using the HTML formatted receipt option, you can copy the shopping cart template to your own template, and edit the section "[-- DEFINE ThankYou_Email --]" that defines how the html email receipt will appear.
The merchant's email address and a CC field where the merchant copy of the order are sent are set under Preferences > Hosting Services
There is no way for the merchant to change a shoppers payment information, only the shopper can do that by signing in to their account in the shopping cart and editing their preferences.
Maybe that sounded a bit strange, but the idea was to be able to go in there and add information about HOW to pay with bank transfer etc. But will work it out in another way then