You can toggle on or off automatic invoice emails on a per-customer basis by using the Email When Invoiced option when editing a customer (see the Invoicing section).
You can create an email template to use for the automated emails by going to Admin -> System -> Mail Templates. Choose Invoice for the template type.
Select the email template to use for automated emails by going to Admin -> Billing -> Company Options -> Defaults -> Invoicing -> Default Automated Invoice Email Template.
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