How are atoms arranged in minerals?
In a uniformed, repeated box-like structure, usually of a single molecule.
Minerals are usually crystallized structures composed of molecules with identical chemical structure. Where as "rocks" are a random aggregation of several minerals together.
The "crystal structure" results from the highly ordered, and repeated structure of "small boxes" caused by the size, shape, and types of bonds the molecules of the mineral possess.
The smaller the size, the denser the shape, and the more ionic the bonds of the molecules are the more packed the molecules will be and the more crystallized the structure will be.
I hope that clearly answered your question.