Just learn the most used one, usually the first one. The most used kanji usually have more readings, not all of them used day to day, just learn the most common first.
I learn kanji by the word, and not the actual kanji itself. For example, I know how to say 面白い(omoshiroi, interesting) but I don't know the other ways in which the two kanji itself are pronounced. I don't know if I should learn it that way, but I find it much easier to learn kanji like that. I don't have to worry about the kunyomi/onyomi that way. Hope this helps :) 頑張って!
@joker12332: oh yeah, that's Japanese for you xD suggestion: try not to stress too much over the on- kun- readings, but rather focus on the meaning of the kanji and the most common ways of reading it.
Like Acidron says, don't stress over all the different readings. It's best to lock in what reading you should use by combining your studies with some basic reading. You could try following some Japanese twitters and practice reading some of the kanji they use in short segments. Hope it helps.