Welcome to Gaia! ::

Have you checked out either of these:

Anki - It's a flashcard program that has a couple of pre-made flashcard decks, including a Heisig one. It also has some special method for reviewing that is supposed to be more efficient (explains it on the site)

Reviewing the Kanji - This site is devoted to Remembering the Kanji. It too has flashcards and a similar method for reviewing, but on top of that, it has different stories for each kanji that people submit in case you're having trouble coming up with a good one, and it has a forum for people studying this book. You can also write in your stories on there to keep them organized for yourself. (You can search the keywords). I only just joined myself, but I think it's wonderful! (Some of the submitted stories aren't completely clean though)

OH
MY
F*
GOD

Thank you. This is soo help you TTwTT Thank you for all the time and effort you put to make this happen for me and so many others. This theard is so helpful for me ;w;

The really short version

Kunyomi is how a word was read before Chinese Kanji were introduced to the country, and Onyomi is how it was read after. A general rule of thumb is that when a Kanji is alone you use the Kunyomi reading, and Onyomi when in a compound. There are numerous exceptions to this that my brain is too fried from lack of sleep to explain clearly so here's a Wikipedia link:

http://en.wikipedia.org/wiki/Kanji#Readings