the root level of the site concept is only important when working within Dreamweaver. It is only important when talking about how the Dreamweaver Site is defined.
It has no bearing on how PowerStore is uploaded to the remote server.
For editing the template within Dreamweaver, the PowerStore files must be at the root of the Dreamweaver Site
You can configure the remote server section of the Dreamweaver site definition to upload the files to the store sub directory though.