Yes, you will have to create two different folders with the same files connected to the same databases. After that you will have to go to your 'jp' and edit all the .tpl files from your template's folders. There are two different folders which are on the core/templates and on the lib/skins/your_skin_name.
Personally i believe that it would be very difficult as you will have to make duble changes on your phpvms site. For example, if you want to install a module, you will have to install it two times...