The placement of Crystals is determined, somewhat, by the difficulty level of the mission. Playing a level on the highest difficulty will result in crystals placed very near spawn points of Titans. Alternatively they'll be placed closer to your base on easier levels, so that they are out of the marching path of enemies.
Only 4 Refineries may work on a Crystal cluster at one time and the amount the cluster contains can be discovered by hovering over it.
Harvesting all of the crystals on a mission will earn the Efficient Medal, worth a bonus $500. If you do not harvest all of the crystals, you will scavenge 10% of whatever is left after the mission ends.
Extraction of Crystals can be enhanced with the following technologies and buildings: