I'm having just a smidgeon of trouble in dealing with this. I feel a little restrained in how I can actually punish the players in story mode. I feel that stress is probably the best mechanic for this, but I have a certain amount of difficulty stopping them from just saying "ok, I stop and have a scone or something" which would realistically give them the breather they need to regain lost stress. So, really, I'm worried about stress, fatigue and changeovers between story and encounter mode that might interject or cause difficulty in maintaining set numbers of same.
P.S. The writer of this helpful note has plenty of tokens, dice and fiddly bits, but does not need an extra sheet to try and hide behind his GM screen, I am more than likely inclined to use the peice of information that is short, simple and easiest to remember/apply. Just think of me as a slightly claustrophobic goldfish.