Transactional email needs to be enabledTo be able to use transactional emails in the connector, you will firstly need to ask your dotmailer account manager to enable dotmailer's transactional email service within your account.
With the dotmailer for Magento connector, you can make use of dotmailer's transactional email service to send, manage and track all of your transactional emails. By doing this, you'll be benefiting from dotmailer's high deliverability rates and reporting and analytic tools.
For more information and guidance, read 'Using transactional email'.
Using dotmailer's transactional email
The Magento integration uses the simple sending method of SMTP and is purely a delivery mechanism for all the transactional emails you already have set up in Magento under System > Transactional Emails. dotmailer doesn't provide any ability to edit, manipulate or design any of your transactional emails.
By using dotmailer's transactional email service, you benefit from not only improved deliverability of your transactional emails but also greater visibility and insight into the sends, opens and clicks for these communications.
All transactional emails sent from dotmailer must use a custom from address that is already set up in your dotmailer account. If the from address set up in Magento does not exist in dotmailer then we will alter the transactional email's from address to your account's default from address.
It is also important to have set the 'unknown mail forward' on the from addresses you use in dotmailer to ensure that any replies to your transactional emails are forwarded on.
Please comment underneath with any questions you may have.
The above also applies for Magento 2.0, with the only difference being that the 'Transactional Emails' section is found by going to Stores > Configuration > DOTMAILER > Transactional Emails.