Tzunami Deployer is a content migration tool. Therefore, layouts, themes, and templates in general are not part of the content and, therefore, are not migrated. However, you can create your own custom templates that include all those elements in the target SharePoint and use those templates in Tzunami Deployer. Tzunami Deployer has the capability to read custom templates. For example, as shown in the screen shot below, you can select your custom template from the drop-down list of available site and list templates.
For more information, please contact Support@tzunami.com