내가 vs 나는 : I ~ 네가 vs 너는 : You ~ 꽃이 vs 꽃은 : flower ~ 물이 vs 물은 : water ~ . . .
이 / 가 and 은 / 는 : They are subject-making investigations. However, the distinction between these is hard to explain even for Koreans. I've heard some Koreans explain it, but it's also not accurate and very difficult to understand. I think the only solution is to get to know by yourself by reading Korean sentences a lot.
But this has a distinction rule. 앞 글자가 받침으로 끝나면 "이 / 은" --- 꽃이, 꽃은 / 물이, 물은 앞 글자가 받침없이 끝나면 "가 / 는" --- 내가, 네가 / 나는, 너는
When I explain grammar, I have to use a lot of jargon, not everyday terms. But I can't express it all in English. The place I wrote only in Korean above was because I didn't know how to express it in English. So I'm going to stop explaining at this point. I'm sorry. I hope it helps a little for you.