For me, the foundation I got from ochem class is what helps the most.
I read through Kaplan entirely and made a flashcard for pretty much every single reaction, idea or thought. Easily 700 ochem flashcards. Force yourself to go through the flashcards over and over and over. I hate going through my flashcards, but if I sit down and force myself through it, it definitely helps.
When I'm going through flashcards, I put ones that I get correct with no hesitation in a pile and the ones I hesitate or get wrong in another pile. That way if I pick up the stack I am only looking at ones I had trouble with at first, in case I don't get through the whole stack.
Then I read through the Kaplan Ochem again with my textbook referring to it constantly. I pretty much read through my textbook or at least 50% of it in depth. This helps explain stuff really well, obviously. For me, being able to faintly recollect the mechanism helps to remember the reaction, especially for the specific stereochemistry. I also looked through my class notes extensively, rewriting some that were a mess and just organizing everything.
Then I began going through Destroyer. I get about 8 out of 10 correct and totally get it. Anything I am fuzzy on, I make a flashcard and add it to the top of the pile.
That's just the way I've been doing it. Don't know if its right or wrong, but it seems to be working. Catch with the flashcards is I have to force myself to do them, they are very easy to make and ignore, but they help cement everything. Repetition, repetition.
Oh yeah, I also have a notepad, so any ideas or thoughts that come up, like tonight, I suck at naming bigtime. I don't feel like going over it tonight, but don't want to forget about it, so I write down a note about going over naming, which I will tomorrow.
Make sure to look at the stuff you DON'T get. Spend your extra time with that, not what you got down pat...