EK is really good, but if any area might be slightly lacking I think it's orgo. I didn't have too much of a problem with it as I took the MCAT the semester following the second half of O-Chem (which incidentally had a final exam that was comprehensive of both halves of O-Chem, so I had a good background).
I was not a fan of the EK orgo book (can't say anything about 1001, as I haven't read that one). Far too cursory! The most useful thing I got out of it was the set of flashcards. :/ Instead, I used David Klein's Organic Chemistry as a Second Language in concert with the official topic list.
yeah, honestly, the EK organic is probably the worst in the batch. they say it and treat it as just a necessary evil of the mcat. i'm glad i paid attention to the concepts in class, the EK book wouldn't have been enough for me,.
Organic is one of the few classes I took that actually used a decent, helpful textbook. No, let me rephrase that-- Wade's O-chem is AWESOME. It's like the one textbook I bothered to read word for word, and do all the problems in the text. (Well, at least the problems interjected in the chapters.).
For many of my other courses (physics included), I was far better off getting some kind of manual that helped me with solving problems, and learning things that way. But if you're having problems with o-chem and want a good reference text to actually gain some depth of knowledge... I would wholeheartedly recommend checking out Wade's O-chem: