Every facility has a quality level (I, II or III), which is shown after the facility's name, either in its window or its icon tooltip on the main menu. That marker defines the development level of the facility: level I has a relatively bad time ratio and high cost of operation, level III quite a good time ratio and low cost of operation. Search for the most economical solution by traveling between terminals!
At present, all facilities can only handle raw materials and commodities that are located in your private storage, so you need to store required materials there for any job you want to run.
Raw materials exploited on Nia need to be refined into commodities in order to create items in the factory.
To begin refinement, just choose a commodity from the selection in the right side of the window. Below the commodity's name you can set the amount to be created. The default amount is the maximum available which can, of course, be modified, and in case you set a higher quantity than you can afford, the available amount counter turns red.
The delta number is a measure of efficiency that shows the difference between the optimal (100% efficiency) and your current requirements. For example, normally, you need 30 pcs of titan ore to create 1 piece of titanium, but only at 100% efficiency. An Agent's initial rate is lower than this, so the refinement quota for a rookie Agent can be as high as 40 titan ore/titanium.
Fortunately, you can improve this rate in three ways. First, you can improve your relation to the facility's owner by completing assignments. Second, you can install additional refinement extensions. Third, you can search for a refinery with a high facility level. It is possible, with enough work, to beat the delta and exceed 100% efficiency, cutting the required components down even further.
Additional parameters that affect your total efficiency.
Relation ratio - Improve this factor by reaching a good relationship with the owner of the facility.
Material ratio - Improve this factor by installing extensions that affect the material efficiency of the process. This value includes the abovementioned relation ratio.