What To Do With Too Much Of One Resource, But Not Enough Of The Other?
A: If you find yourself in a situation where you have a lot of unneeded crystal or metal, but you have too little of the opposite resource, then it's time to start building Manufactories. Unlike in many other RTS games, there is no "market" for selling off your existing excess crystal/metal, but by adjusting your inflows with Manufactories you can re-balance your economy.
A Metal Manufactory will produce 8 Metal per second for you, at an expense of 12 Crystal per second of income. Crystal Manufactories work the same only in reverse. You'll never want to have both metal and crystal manufactories running at once in your economy, since that would be a huge waste. But expert players often do have both metal and crystal harvesters in play at once, with just one group or the other paused. A paused manufactory neither produces nor costs income.
Often if you need a resource fast, you can build a lot of manufactories and get what you need, then pause a bunch of them once you have what you need. You can exert a large amount of influence over your economic situation with techniques like these, but it depends on what your specific needs and goals are, and how much economic micromanagement you are interested in doing. With good planning and good defenses, you really shouldn't need to be micromanaging your manufactories -- after all, the most purely efficient economy won't use any manufactories at all. But in practice, manufactories are great for making short-term adjustments (at some efficiency cost).
If you find that you wish for a long term balance adjustment (say by having more metal than crystal harvesters and tend to use far more crystal than metal due to your ship constructions) you can upgrade your metal harvesters and then leave several crystal manufactories on all the time. An 8:5 or greater abundance to lack ratio in harvesters upgraded in this fashion (e.g. upgrading 8 metal) is about 5-6% more income than upgrading the harvesters you lack (e.g. upgrading 5 crystal).
Generally, manufactories will manage themselves. That is to say, if you are running incredibly low on resources (less than 10,000 of either type) the corresponding manufactories will turn on automatically to help construction. Of course, if you are low on both resources, it would be a waste to try to convert both materials to the other one, so no manufactories will run. You can turn off this behavior on the Ctrls window, it is about half way down in the left column.