This depends on how you've set up your version control, but generally you would put your entire project folder in version control, so that anything in that folder is covered. (I.e., both the .xcproject and the .xcworkspace files would be.)
Of course, how you set up your version control repo is up to you, but I would recommend something like the above. I can't offer specific help for various version control systems though, as they're made by third parties, so I recommend referring to the documentation for whichever system you're using.
