I do option #1. It does take time to look through the cards that match what you've been taught in class, but it makes going through zanki much easier while helping you study for class. Then at the end of the block, let's say biochem, whatever cards are leftover that weren't covered in class I move them to my main deck and start doing them. I remember the biochem deck being ~1800 or so including the vitamin deck and there were only about 400 cards that weren't covered in class that I needed to do on my own. You can either brute force these or if you have the time watch BnB/youtube videos to help strengthen the understanding of these cards.