I think your misconception is that it has to be one or the other, when in fact, every kanji has kunyomi and onyomi readings. The most frequently used kanji can have a lot of readings, but normally it's between one and three. Don't worry about the readings too much, you'll do better if you learn the readings when they are actually used in a word.
But if what you were referring to was whether the kunyomi or onyomi reading is being used in a word, then it generally depends on whether it's one kanji by itself (kunyomi reading) or multiple kanji forming a word (onyomi reading).
October 23, 2016 at 3:07am