If you have turned on any of the Pay Later settings under the Financial Information section of the Event Settings tab you will notice that you have two separate versions of the Thank You Message. 

• The first version will be labeled "Thank You", this thank you message will be used if the event registrant submitted their event transaction with payment. 
• The second version is labeled, “Pay Later Transaction” and will be used if the event registrant selected the Pay Later option when submitting their event transaction.

Having these two separate versions of the email will allow you to customize the content so it is specific to whether payment was made during the transaction or not.

To edit the "Pay Later Transaction" email template you will select that tab and then click the Edit Message button on the bottom right corner of the screen. All the features of the email template editor will be available to you including the ability to insert in mail merge fields from the transaction.