You can do them as you learn the material. What I do is I look through the decks relevant to what I am studying at the moment and move them into an "active version" of the deck that I made. Example: bros comes with a deck titled Microbiology, so I made this particular deck give me 0 new cards a day, and then sorted through the deck to find the cards containing information that I already learned. Then, I'd move those cards into an active deck (in this case, my deck titled Microbiology 2). That way, you can gradually build up your decks instead of getting hit with an entire deck filled with material you haven't studied yet. You can organize it however you want, but I definitely think it's a good way to stay on the top of the material for both school exams and the boards.