The basic breakdown of the new ESS system is that in systems with the ESS present, a portion of it is sent to the bank; if no one steals it, it’s paid back to you. However, if the jackpot gets juicy enough, people will try to take it and there will be many a gud fite for the loot.
There’s also a smaller reserve bank that doesn’t empty and just keeps building until someone tries to break into it with a key; that feature will open up a bit further down the road (to get those sweet sweet payouts built up… or something far more sinister? dun dun Duuuuuun!)
Hope that cleared it up a bit for you; once you play around with it a little, I think (hope) you’ll find it’s pretty intuitive.