I'm new to the game and I don't understand one thing. I know that you can subdue someone and hide the body, so it will balance the negative effect of subduing and positive effect of hiding, but are you able to beat the game or even level without having any negative score throughout it? Is it possible or you just have to get some negative points for an action and choose which negative one to choose in order to beat a level? Or maybe you really can find everything you need to not get any negative points?
The following answer is based on my experience with the Hard difficulty, and only the Hard difficulty.
The only way I know of, where you can beat a level without any negative points, would be to kill your target without interacting with anybody in any way. Which means: Do not subdue or kill anybody except for your target.
However, if you manage to hide the body of a non-target after subduing or silently killing him, the points you get from hiding the body completely negates the points you lost from subduing him.
Keep in mind, though, that killing a civilian removes an additional 6000 points, which cannot completely be nullified.
On a semi-related note: Hiding a body does not kill, regardless of the hiding spot. So after you subdue someone, you can push his body off a cliff to hide the body and he will not die.
If you are playing on anything less than purist you don't need to worry about it unless you want the silent assassin rating, in that case just sneak around people and distract them with throwable objects, but if you want the highest score possible you have to get all the challenges first to increase your multiplier then do it on purist without interacting with anyone like Prostynick said, and as Diana said "It's entirely up to you" , just have fun and do it anyway you feel like.