On the setup of your membership page if you have turned on 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 “To Purchaser”, this Thank You message will be used if the member submitted their membership transaction with a complete payment. If there are gift memberships, the second tab would be labeled "To Giftee."  If Pay Later was an option, another tab with “Pay Later Transaction” and will be available. Having these 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 blue, “Edit Message” button on the bottom right corner of the screen. All the features of the normal email editor will be available to you including the ability to insert in Mail Merge fields from the transaction.