The location of the Eternia Crystal in each level varies, but is located to make the enemies have to travel a decent distance to the crystal. It is common to see the crystal in the center with multiple access points. In certain challenges, the Eternia Crystal does not exist.
The origin of the Eternia Crystal has to do with the parents of the four playable heroes. They banished an immortal evil called the 'Old Ones' inside the Eternia Crystals and now their children must stop the hordes of enemies from unleashing the evil that now resides within them.