When you are crafting the email message body you should use regular edit option for the plain text email, then select the html email and use the DW edit button to setup the html body of the message. When you are editing with DW you just need to save the page and it will return you to the wizard so you can preview the message. You should specify ok in the wizard after this then test the page out.
This should create a single file for the email in your WA_Universal_Email folder, it should be named WAUE_pagename_1.php.