Mathijs:
Would it be recommended to reserve Manu beforehand, or is that something to do in Cusco like some reviews are saying?
For Manu, you need to reserve beforehand because these are multi-day trips and they don't leave every day. So, unless you're prepared to wait around in Cusco for days, planning-wise, it makes more sense to book beforehand.
For the Nazca flights, I had no trouble booking the night before, but that was in 2011.