Generally speaking, you won't be able to precisely balance exactly what your inflows and outflows are, as Ranakastrasz says. So at some point you're going to hit a point where you have very little of one resource and everything is stalled, while you have such an incredible abundance of the other resource that you hit the cap and then your income starts getting wasted because you can't gather more than the resource cap.
The manufactories are something of a safety valve, for when your economy is out of balance. If you notice that a ton of them are on, the solution isn't to turn them off -- that's like turning off air bags because you keep crashing the car and they keep deploying. Instead, the solution is to leave the manufactories on auto, but then to fix the underlying problem (ie, stop crashing the car). In this case that means either increasing production of a specific resource, or reducing consumption.
More often than not, though, if you try to make a "perfect" economy that is exactly in balance, you'll spend so much time doing that that you're ships will hit ship cap, and thus production will stop because there's nothing left to build, and thus resources skyrocket and hit your resource caps, and then you wind up with titanic amounts of wasteage based on not building enough.
