grammar - Use of 'not' in questions

When is it okay to use 'not' when posing a question? I believe that the person asking would include the 'not 'when he believes the implied to be true. For example: "Are you going to the store? "Are you not going to the store?"

Then the question of how to properly answer it. "Yes, I am going to the store" "No, I am going to the store."

and if they arent going... "No, I am not." "Yes, I am not."

I wonder if this is a French rule and therefore confusing to English speakers; where 'Si' is used instead of 'Oui'.

Anyways, your thoughts?