Honestly it depends on what you hope to acheive through your Qbanks. If you're trying to learn info from them, definitnely make flashcards/do them throughout. If you are trying to get experience with Step 1 style questions after you "learn" your class info, then I'd wait until closer to your exam.
Personally, I've been using Kaplan along side my organ systems as "throw away questions." As in I'm using it to test my knowledge, and I'll review explanantions of the questions I get wrong, but won't spend hours on it. In addition, I'm doing semi-mixed Uworld questions almost every day to start reviewing material for the boards. Granted I haven't taken step yet, so I don't know if this strategy will work or not.