There are two parts to your question:
First, one has to ask how the atoms arrange themselves with respect to one another at the microscopic level. This information is what people usually refer to as the "crystal structure". Usually, the arrangement of atoms is periodic - it repeats in a pattern, so we typically visualize the crystal structure in terms of the smallest repeat unit, which is called the "unit cell". The crystal structure that nature chooses will usually be the one that minimizes the free energy, and as such it can be predicted in theory. It turns out for simple materials (say pure Copper), this can be done pretty straightforwardly as long as you have a good way of computing the energy of various configurations, and make some assumptions about the number of atoms and size of your repeat unit. For more complicated systems, it turns out to be difficult in practice to predict the crystal structure, because there are so many possibilities to try. This is an active topic of research.
The second part of your question concerns the macroscopic "shape" of a crystal, which depends mostly on the growth dynamics, which could depend on many factors, one of which is the crystal structure. You can imagine when you are growing a crystal that it starts out small, and then additional atoms or molecules (say in the gas or liquid phase) have to come nearby and stick to the surface. Some surfaces may be more attractive to the nearby atoms or molecules, so a crystal may grow faster in particular directions, and this is what determines the overall shape. Some of the factors that affect the growth can be controlled - it is a real art to be able to grow a crystal with a certain shape. As far as I know, Wulf's construction predicts the equilibrium shape of the crystal, which is often not the way the crystal comes out when you first grow it. One thing you can say for sure is that crystals will have some symmetries at the microscopic level. The growth along any two directions related by symmetry should occur at roughly the same rate, so often if a crystal has a macroscopic symmetry, this will be related to a microscopic symmetry. The usual example of this is snowflakes, many of which have hexagonal symmetry (they look the same if you rotate them by 360/6 = 60 degrees). This is because the crystal structure of ice has the same symmetry.
Hopefully this has answered your difficult question.