How to deal with multi enviroment project setup

Hi,

Im new to cocos2d-x, and I have a question about multi enviroment project setup. I’ve crated a project template using create_project.py from tools folder. Everything works fine, Im able to run projects via Visual Studio 2012 on Windows and XCode on Mac. But there is one thing that I have a problem with. When I add a new class via VS or XCode it doesnt land in Classes folder on disc. XCode folder tree shows the file in correct place, but files are not in Classes folder phisicaly. Is there any way to configure it?