Since you have eCart 5 and Universal Email 4, you can run through the check out wizard which will not have the email step. But you can then add the email separately using Universal Email. You will need to apply Universal Email to the confirm page.
When you open Universal Email you can create the Email template by clicking the DW button, and then you can drag the eCart columns from the Bindings Panel, which should have of all the eCart columns listed.
Let know if you have any questions or if you want assistance in setting the email correctly.