Hello Sean,
You can customize this behaviour in the file:
\CMSModules\Ecommerce\Controls\ShoppingCart\ShoppingCartContent.ascx.cs around
line 515 where the following methods are used:
OrderInfoProvider.SendOrderNotificationToAdministrator(ShoppingCart);
OrderInfoProvider.SendOrderNotificationToCustomer(ShoppingCart);
Another way could be to disable notifications and create Global Event Handler which will send e-mails via the code.
Best regards,
Martin Danko