Jisho is good. Rikaichan uses the same vocab as far as I know so you're good to go.
I never once sat down to learn on/kun readings individually. I should probably get around to it nowadays but for a beginner, I would not recommend it. I just learned various readings as I went along, they came naturally from a variety of compounds I encountered over the months/years. So yes, I more or less agree with that.
I also blogged about this a while back so if you're interested, feel free to
give me more page views check it out:
http://gareblogs.wordpress.com/2013/...-niche-medium/ 