Hmm, I think that the V-Sync in game will be exactly the same as the V-Sync in NVCP. If you see nVidia's default settings, it's "Use application's settings" which means it's up to me in game if I wanted to enable/disable the V-Sync.
The V-Sync settings in NVCP is just global if I want to set it on all games regardless. I believe that in game settings should be find and just as good.
So I guess I will just do that.
Thanks for letting me know that V-Sync ON is okay to be combined with G-Sync.