Yes negative questions can be confusing. Generally negative and positive questions mean the same, but a negative question usually implies that the person asking the question already knows the answer or assumes something and is just making sure of something. For example: Isn't that nice? ( I think it is nice, do you agree?) Don't you have any money? ( I think you don't have any money) Wouldn't you like a blanket? ( I think you are cold) Haven't we met before? ( You look familiar and I think we have met before) Positive questions are just ordinary questions and the person asking it really does not assume anything.

okay, let's see haven't we met before? it means you trust that you and he/she have already met in 80% for sure. and have we met before? it is some 50%, because you just do not know.

I'm surprised that you are confused, since japanese speak the same way!, it is the same as ending a phrase with masenka instead of masuka.