Rule of thumb is kun’yomi when it’s alone, and on’yomi when it’s part of a compound kanji, but yeah, there’s practically more exceptions than there are words than follow the rule. (Though the exception to the “always exceptions” rule is that kanji followed by okurigana – i.e. hiragana permanently attached, like verb endings or whatever – is always the kun’yomi.)
Rather than learning “this reading goes here, this reading goes here”, a better way to learn it would be to learn vocab. “This word is read like this.” You start to get something of a feel for it over time, but learn words rather than rules.