Select the Layout you want to use. When the job is finished processing, there will be a version created with the selected layout.
In the Job Details Page
Click on the job name from the Job List to go into the jobs detail page.
Locate the Cloud Layout option in the job details and click on the down-arrow.
Select the layout you wish to use.
After selecting the layout, click on the "Regenerate with Layout" button.
You will now see a new version of the transcript created that contains the layout and template.