Just remember if you're going for one playthrough, you must only use none lethal takedowns (tap ). Doing so will not void the 'Pacifist' achievement and will also increase the counter for the achievement 'Consciousness is Over-rated'.
Right from the first mission, you'll be introduced to how to take people out, so from here I'd recommend you try and get your 50 takedowns as and when you can. If you see an opportunity, then take it but don't rush. It's easier to do this achievement at the beginning of the game rather than later on when it could become more risky for you.