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.