During setup, each player gets 2 tokens each of oxygen, syringe, and blood, 4 of each of the others. There are a few extra tokens in the box--those I assume are just in case you lose one or two. But I don't make them part of the game play at all; I actually bag up each player's set of tokens separately (so the bag contains 18 tokens per player).
The way I read it, all the tokens go in the matching symbol spot on the mat. Then each player starts with 2 active supplies (that don't have to be prepped using cards) and I assume those go in the Medical Cabinet. The GenCon overview video shows the setup this way, anyway, and that's also how the rulebook shows them.
Regarding the patient deck, I got this answer in a different forum.
Smirk & Dagger Games *
09-27-2017 at 9:37 am
Good question. Yes, discarded Patients can be reshuffled. Normally this will take care of it -- but, in the rare case that all Patients are used, pause the game after a player completes their turn. Tally player scores to this point and then reshuffle the Patient cards to form a new deck. Thanks!