I did the Becker lectures and the sims for that section until I did the whole book, then I did the NINJA MCQs. I have done them subject by subject, but for the software to really work the way it is intended, doing sets of 30 mixed gives you the best analysis of where you are, plus the actual exam will be mixed, so its great practice. I see your point about wanting the questions to match the sections you are studying, but in reality, doing the mix is more like the real exam. I always did the MCQs for a couple weeks before exam and took notes on what I missed. If I needed more info, I would look up the subject of the question in the Becker book.