You're supposed to embrace the chaos and collapse. Seriously, that's the point of the game. I think we tried to hammer home how the Player Best Practices demand this in other threads, and the interlocking systems are indeed supposed to make it hard for your fledgling crew to thrive (that's literally the point of the game after all). Indeed, teh first entry in the Practices (Embrace the Scoundrel's Life) directly addresses everything you just posted.
There's a reason most FITD games after BITD + other inspired designs like Daggerheart (and indeed even NSR games like His Majesty the Worm) move the "player expectations/practices/etc" right up front now. These are a set of behaviors that lead to the best outcomes with the mechanics as designed.