Soul crystals are intended for learning magic initially. It means they are mostly earned when you level up.
If your Magic stat is 2, you receive 1 crystal each level. You receive two crystals with Magic 5. You receive three with Magic 8.
You can also meet Golems, feed them ice cream and ask for help, but it won't be much. You can defeat final boss with ice cream to get 20 crystals, but that's pretty stupid.