If you do a test purchase using the VirtueMart component for your Joomla eCommerce shop, then you will see that the customer will receives an "order confirmation email". 

If you want to change or customize this email, you will not be able to do or see this email in the Joomla admin.

This order confirmation email layout is define in code in the TPL template file ...

/components/com_virtuemart/themes/YOUR_VM_THEME/templates/order_emails/confirmation_email.tpl.php

where YOUR_VM_THEME is your virtuemart template.

Parts of the dynamic content of that email is generated by the function  email_receipt() in the file ...

/administrator/components/com_virtuemart/classes/ps_checkout.php

And in there, you will see code such as ...

$VM_LANG->_('PHPSHOP_CHECKOUT_EMAIL_SHOPPER_HEADER1',false)

What this is doing is pulling the language text used in the email header.  This text is defined in an array key value pair where PHPSHOP_CHECKOUT_EMAIL_SHOPPER_HEADER1 is the "key" of the text is the "value" of the array $langvars.  

Assuming that your site is set to the english language file, you will find this array $langvars in the file ...

/administrator/components/com_virtuemart/languages/common/english.php

So if you want to change the text of the order confirmation email that is being sent to your customers, change the text in that file.

To change the customer registration welcome email, see this tutorial.