You use 는/은 as a topic particle, and 을/를 for as an object particle. Let me give you an example:
저는 사과를 먹었어요. = I ate an apple.
저 = I
사과 = apple
먹다 = eat (in this example, 먹었어요 is the past tense form of "eat", so it would be "ate")
In this case, because "저" is the topic, then it also is the subject. It means that "저" is the one who "먹었어요" ("I" am the one who "ate"). "사과" is the object because it is what I ate. The apple is not eating. It is just the object that I ate. So we use 를 to indicate it is the object.
I hope that my explanation makes sense to you?