I have separate notebooks, one for each subject, and took down notes for every chapter in the TBR books (but also supplemented my notes with tprh and ek books). The reason being that it's just the way I study, and I've been doing it my entire undergrad so i'm really much more comfortable doing so. I also think it's a personal preference. If you feel like you'll retain more making your own notes ( i feel the same way) but that it might take you longer, then maybe take that into consideration when you plan your day-to-day workload. Spend a few more hours maybe? Remember, you're simply following a study guide, but everybody learns differently, so follow it and make adjustments according to your own study habits to make it more effective for YOU. Goodluck!