Personally, I only memorize kun reading of a kanji. If a kanji has lots of different kun readings, I choose 2 kun readings that I can encounter more than the others.
I don't memorize on readings. I learn them while learning new words.
I agree with Aniumixie's approach. Don't bother too much with the on- reading as the rules are sometimes a bit loose with those anyway. Learn the main kun- (or more than one) and learn the on- when it comes up with other kanji.
I also try to write each kanji at least 10 times each. It helps me a lot when it comes to remembering them, but I also use physical flashcards on the side for when I'm commuting/travelling.