Ideally how it will work is the reverse of what we currently have, as currently the visual aspects are done first and then atmospheric and gravitational characteristics are done.
In a perfect system we would generate the overall planets mass, and then calculate what materials the planet has and how much of each. Gravity is based on overall mass, and atmospheric density based on the existence of certain materials and their percentages of the whole. After the materials are calculated the colors and textures of the planet would then be generated. Which means a player could get some idea of what resources they could expect to find before ever landing and testing the surface.
We will not have a terrain deformation system for planets(only for asteroids) so all mining takes place on the surface. Which means that all the materials must follow some sort of map for their propagation over the surface.