Yes. Now it there is literally no economic reason to not use the auto-manufactory management functionality (that is on by default).
I quite frequently run into a situation where I need (or want) to manually manage them. Often it looks something like this:
I have 100,000 crystal.
I have 200,000 metal.
I am gaining resources at -500 crystal / +100 metal due to some crazy turret production or something, usually a short term spike in costs.
If I don't manually enable crystal manufactuaries, I will run out of crystal and stall. If I run the crystal manufactuaries on from the start, I can avoid that situation.
Though if I did have enough manufactuaries to produce 500 crystal to counteract the drain it wouldn't be important (would need over 60), but manufactuaries also have a cost, and I can manually advert meltdown with considerably less than that.
You won't stall, that's the whole point. Assuming that you have enough crystal manufactories (I like to have around 30 of each, but sometimes need as much as 45 of one), then they will kick in once you are sub 1,000 stored crystal, and will start draining your metal.
Assuming that your turrets or whatever are finished before you run out of crystal AND metal from that process, then your economy will go back to normal and the crystal manufactories will turn themselves off. If you do wind up running out of both resources, then you'll stall out and all the manufactories will turn themselves off to avoid making the situation worse (but nothing would have saved that from stalling out on the production side, in that scenario -- you'd need to adjust your expenses instead of your production).
There's absolutely no reason to carry a big ongoing balance of metal or crystal, since you're able to adjust both income and expenses as needed. In terms of absolute gross metal + crystal income, your income is best by always letting the sort of algorithm employed by the auto-manufactory management, rather than trying to use manufactories preemptively to keep a large balance of one resource or the other. It turns them on at the last second in order to avoid using them at all if at all possible, since they do come at a cost, basically, which is something exceedingly hard to do by hand.
