Oh, if you're just using it for checking then it's absolutely safe. The Pokémon never actually leave your game (unless you mess it up and accidentally send them to the real GTS, which is why I always ask for an impossible trade just in case), and if you set your DNS back to Auto once you're done then there's absolutely no evidence that you ever used it.
Check out Smogon's new Doubles
Black 2 FC:
My Pokécheck Pokémon
RNG is kind of like firing a gun. Why shoot blindly in every direction until you're lucky enough to hit the target when you can just take the time to aim properly and hit it with one shot?