To assign a version control system to the project root:
VCS -> Enable Version Control Integration or press Alt + Back Quote and select Enable Version Control Integration ....
In the Enable Version Control Integration dialog box that opens, select the version control system from the drop-down list that you want to associate with your project root.
From there, your project will be connected to the version control system that you want to use. You can right-click on the directories that you want to include in VCS and go to the version control system. And then add to VCS.
For example: Subversion -> Add to VCS or Ctrl + ALT + A
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