kanji - When am I supposed to know when to use the On-Yomi (sound-element) or Kun-Yomi (meaning element)?

I'll just start off by saying I'm not exactly new to Japanese but I'm still learning the kindergarten equivalent of what native speakers learn. I've mastered Hiragana and Katakana and am using Genki to learn my grammar and Kanji. One thing it fleetingly explains and that I'm still confused about is the difference between On and Kun readings. I understand that On is for the Chinese benefit and the Kun is the reading the native speakers made for their speaking, but when making compound Kanji, there doesn't seem to be a pattern between the usage of On or Kun. It says that On is also the "sound element" and Kun is the "meaning element", so how am I supposed to know the difference between when to use either one??