When do I use "na" or "nicht" in German?
na gut vs
nicht gut, is there a difference? Which is grammatical?
Na klar vs
nicht klar, are both grammatical?
The examples you listed have a different meaning.
"na" isn't a negation. It doesn't mean "no" in any way. "na" doesn't change the meaning of what you say, it just changes the tone. It mostly acts like a reinforcement of its succeeding words. You can always leave it out, it's somewhat redundant.
"nicht" instead has a very clear semantic meaning, it negates the succeeding word.