> Another thing troubling me is whether to reply yes or no on questions like "didn't you agree?"
Native English speakers often get confused by this one too. You can respond either yes or no in those situations as long as you specify the one you wanted afterwards.
e.g. "Don't you agree?"
"Yes, I agree" and "No, I agree" would both be acceptable.
I've heard of many situations where East Asian students of English cause confusion by answering "Yes. Yes, I don't agree." — which doesn't sound natural in English.
Native English speakers often get confused by this one too. You can respond either yes or no in those situations as long as you specify the one you wanted afterwards.