Do you want to have the same thing as in
www.mywebsite2win.com that propose the possibility to create websites with different looks.
In this case, you have to prepare as many JMS Template for each Joomla template and let your customer select the package that they want.
If you want that your customers have their own joomla templates and be able to install their own joomla template then this is the video CP-05 where you specify that you want to "copy" the /templates directory and that you want the "template folder" = {deploy_dir}/templates