Post in the making. I'll explain the Chakras system.
Note already: when you have selected your first line of power for your character, you'll automatically get a selection of decent Chakars.
They are in your inventory!
You must open your character panel (p key) and your inventory (i key) and equip the chakars (r-click a chacra to equip it or drag and drop). The chakras automatically go to the right slot for them.