Keith has reams and reams of story that haven't been integrated into the game yet, and even I'm not aware of the details of all of it, honestly. But in general, all magic flows from the Ilari, which are these larger noncorporeal beings that you can interact with through their various guardian stones (the crystals you refer to). The crystals themselves are just objects, but they are conduits to the Ilari.
Similarly, the glyphs are given out to various people in the world from the Ilari, and when one person who was a glyphbearer dies, that glyph passes to someone else. People without a glyph who stay out in the world, beyond the protection of a guardian stone or a neutral Ilari stone at worst, quickly go crazy. Many of them turn into some sort of evil monster, some don't.
There are also Dark Ilari that are not benevolent at all, and they're responsible for most of what is going on with The Deep. And there's some other faction of Ilari that I forget what they are called, but they are more wild and untamed rather than distinctly evil.
In terms of what actually happened to the world (what caused the breakup and reforming of reality), that's something that will get seeded into each world as a mystery to solve as you play through it. And some of that will vary by world.
